In 1648, submitting to the parliamentarian visitors, he was appointed by the committee for the reformation of the University of Oxford to succeed Doctor Robert Sanderson as Regius Professor of Divinity. He declined the post, however, and soon afterwards was instituted as vicar of Chew Magna in Somerset. At the Restoration he conformed, and as there was nobody to claim his living, he retained it till his death on 12 December 1683.
Anthony à Wood says he was a noted philosopher and theologian, an able preacher, and well versed in the Church Fathers and scholastic philosophers.
He had a controversy with Joseph Glanvill, on the subject of Aristotelian philosophy. Crosse then passed the baton to Henry Stubbe, who became a very persistent critic of the Society.
A book which Crosse wrote against Glanvill was rejected by the licensers, but Glanvill, having obtained the contents of it, sent it in a letter to Doctor Nathaniel Ingelo, who had a hundred copies of it privately printed under the title of the Chew Gazette. Afterwards Crosse wrote ballads against Glanvill with the object of ridiculing him and the Royal Society.