In 1907 he was enrolled by the Guiyang Military Elementary School, and transferred to the more famous Wuchang Third Army Middle School in the following year. In the same year, he was chosen by the Defense Department of Qing Dynasty to study in Japan at the 11th class of Tokyo Shimbu Gakko, a military preparatory academy.
When studying in Japan, he became acquainted with fellow student Chiang Kai-shek. He learned military skills and was influenced by the anti-Qing Dynasty theories of the Tongmenghui, which he soon joined. In 1911 after the outbreak of Wuchang Uprising, He came back to China with other members of Tongmenghui, to work for Chen Qimei, who was governor of Shanghai and also known as Chiang's mentor. When the war waged by the Tongmenghui against Yuan Shikai failed, He had to take refuge in Japan and continued his military training at the Imperial Japanese Army Academy. His classmates at this time included Zhu Shaoliang.
In the fall of 1916, he was given the rank of colonel and named the commanding officer of the 4th Regiment of the local forces of Guizhou Province, with particular responsibility of training Guizhou troops. In Apr 1917, he married Wang Wenxiang, the sister of Guizhou leader Wang Wenhua. In 1920, a power struggle broke out in Guizhou Province, and he sided with Wang, who would emerge victorious. After Wang assumed power, He was given the positions of the head of the local military academy, head of the police forces, and the head of the Guizhou 5th Brigade. Between Jan and Jul 1921, he was the commandant of Guizhou's military academy. In Mar 1921, Wang was assassinated in Shanghai. Finding himself at odds with Wang's successor, which would soon turn violent, he fled to Yunnan Province, where he would be named the commandant of the local military academy in Yunnan in 1922. In Yunnan, the faction ousted by Wang in 1920 attempted to assassinate He, wounding him in the chest and legs; he recuperated in Shanghai at the home of Wang Boqun, He's brother-in-law. In 1924, he was recruited by Chiang to Guangzhou, Guangdong Province, China to assist in the establishment of the Whampoa Military Academy. As the chief instructor of the academy, he successfully led a regiment of trainees in actions against a local warlord Chen Jiongming. Later in 1924, he was made a divisional commander in the newly reorganized National Revolutionary Army. In 1926, he was named a senior instructor at Whampoa Military Academy. In Oct 1926, he was named the commanding officer of the 1st Cadet Regiment consisted of Whampoa trainees, and participated in the Northern Expedition. Later in the year, he was assigned greater number of troops and saw action in Guangdong Province, Fujian Province, and Zhejiang Province during the Northern Expedition.
Early 1927 was key in He's ascend to wider influence, as he began his involvement in national politics, played a leadership role in the bloody purge of communists in Shanghai, and conducted a successful military campaign at the Battle of Longtan (also part of the Northern Expedition) in Aug. In Jul 1927, however, the situation took a risky turn. Wang Jingwei, Li Zongren, Bai Chongxi and others challenged Chiang Kaishek and successfully ousted Chiang, forcing Chiang to exile to Japan. During this struggle, He refused to show support for Chiang, believing that it would not be wise to position himself against the apparent victors in the coup. Unexpectedly for He, Chiang was able to maneuver himself back into power in Dec 1928. Holding a grudge against He for the act of disloyalty, Chiang sacked He (now the chairman of Zhejiang Province in eastern China, a position he would hold until Nov 1928) in Feb 1928 and personally took over all troops previously assigned to He. For the following several months, He would remain in Hangzhou, Zhejiang Province, claiming health problems. In Jun 1928, after being courted by Chiang, he would decide to swallow his pride and return under Chiang. In Oct, he was returned to high position as the deputy director of the Department of Training of the Chinese Army. In 1929, amidst the Central Plains War, his father passed away. Due to his military responsibilities, He was unable to return to his home town to attend the funeral. When Chiang heard of this, the Chinese leader personally attended the funeral in He's place, thus marking the end of their first disagreement. In Mar 1930, he would be named Chiang's chief of staff for military affairs, a position he would hold for many years to come. In Dec 1930, he was further made the head of the political section of the Chinese Army.
In 1931, He led troops against forces of the Jiangxi Soviet, during which campaign he suffered great casualties, and his reputation as a military leader faltered slightly.
As Japanese aggression toward China materialized into invasions in northeastern China (also known as Manchuria), Shanghai, and other locations, he supported Chiang Kaishek's belief that the communist threat must be eliminated before Japan could be dealt with. In Mar 1933, he was made the head of the Beiping Military Committee, which oversaw the defense against Japanese aggression in northern China, replacing Zhang Xueliang. In this role he de-escalated the situation with Japan and engineered the Tanggu Truce. In Jun 1935, he signed the secret He-Umezu Agreement with Japan, appeasing Japanese aggression in northern China so that the Nationalist Party could continue to focus on anti-communist campaigns. During the Xi'an Incident of 1936 during which Zhang Xueliang kidnapped Chiang in an attempt to force him to unite with the communists, He briefly held control of the Nationalist forces. He briefly clashed with Chiang supporters during the incident, including Chiang's influential wife Song Meiling, but after Chiang's safe return Chiang calmed He by giving him the honor of officially speaking on his behalf during a major rally in Nanjing, China.
China and Japan plunged into full scale war in 1937. On the first day of the invasion, He was overseeing a military reorganization effort in Sichuan Province in central China. Rushing back to Nanjing, He Yingqin was made commanding officer of the 4th War Area shortly upon his arrival. Between Oct 1940 and early 1941, He undermined communist efforts in infiltrating the Chinese Army. In Nov 1944, his 14-year tenure of being Chiang Kaishek's chief of staff for military affairs came to an end as Chen Cheng was given this title. Later in the same month, he was placed in charge of the China War Area, which encompassed southwestern China. Shortly after, he was also given party leadership of Guizhou Province. In late 1944 and early 1945, he personally commanded the Burma-bound Chinese Expeditionary Army; in this role, he frequently clashed with Joseph Stilwell, who viewed He as a poor military leader. In 1945, he oversaw a series of Chinese offensives in China, seeing several victories leading up to the end of the Second Sino-Japanese War and WW2 overall. On 9 Sep 1945, he accepted the surrender of Yasuji Okamura in Nanjing, China, representing China and all Allied nations in southeast Asia.
Immediately after the war, He personally interfered with the deportation of Japanese military servicemen from China; while it was initially noted that each Japanese servicemen could only take 15 kilograms of belongs, He attempted to increase the limit to 50 kilograms (ultimately the compromise would be set at 30 kilograms). He also interfered with the inspection of such belongings being taken out of the country, favoring allowing the Japanese troops to leave with minimal inspection, thus he was being accused of allowing some Japanese to leave China with stolen property. He was also instrumental in the lenient treatment of Okamura after the war for that Okamura had good intelligence on the inner workings of the Chinese communists, something that interested Chiang Kaishek. Thus He was accused of being far too pro-Japanese at a time when the Chinese people wanted justice; He would argue that he was re-establishing a foundation for better long term Sino-Japanese relations.
In May 1946, the Chinese military was reorganized with Chen Cheng and Bai Chongxi at the helm, leaving He Yingqin with the mere position of the commanding officer of the Chongqing garrison. Shortly after, he was sent out of China to serve as a member of the delegation to the United Nations. In late 1947, he was recalled to China as the Chinese Civil War kicked into high gear. In 1948 and 1949, he was twice made the Minister of Defense (the second time in acting capacity only); he would resign from this position by the end of the year as there was little he could do as minister when the Nationalist military was falling apart at this stage of the Chinese Civil War. Between Mar and Jun 1949, he also served as the head of the Executive Yuan. He fled to Taiwan in late 1949. In early 1950, he failed to secure any important postings as Chiang formally resumed power again, thus marking the end of his political career; from this point on and until his death, he would only hold the position as a senior military advisor attached to the Office of the President of the Republic of China, which held little political influence. His wife Wang Wenxiang was diagnosed with breast cancer in 1952, but would survive until Apr 1978; in his wife's last sixteen years, they traveled to Japan frequently to receive medical treatment, and He was well known as a devoted husband during her illness. In Jan 1954, he was named the head of an organization that encouraged economic cooperation between the Republic of China and Japan. In Apr 1977, he was named the chairman of the committee that administered the Sun Yatsen Memorial Hall in Taipei, Taiwan. In Jan 1980, he was named the head of the Chinese Red Cross. In the same year, for his 90th birthday, master artist Zhang Daqian presented him with a painting; this painting would remain one of the most valuable possessions to He. In 1982, he was named the first chairman of the League for a United China Under the Three Principles of the People. He was suffered apoplexy during a stroke in Apr 1986 and became hospitalized. He passed away in Taipei, Taiwan, Republic of China in 1987. He was buried at the Wuzhi Mountain Military Cemetery in northern Taiwan.