Mustafayev established the first independent center for analytics in Azerbaijan in 1993. He published the scientific and political papers Dirçeliş XXI asır (Russian: Vozrajdenie-XXI vek). He also found and served as the head of the Human Rights Institute under the Azerbaijan National Sciences Academy.
Having published more than 70 scientific articles and books, he represented Azerbaijan in many international conferences.
Mustafayev’s most well known works are concerning the massacre of Azerbaijanis by Armenians. He researched and archived the Mountain Jews genocide by Armenians too.
Mountain Jews of Azerbaijan have campaigned for the building of a monument in honor of the more than 3000 jews massacred by Armenians during the pogrom of 1918. Some estimates point the number massacred to 10,000.
Following a long illness, Mustafayev died at the age of 48 in Memorial Hospital, Turkey.