Most of his professional career was at the University of Illinois at Urbana-Champaign, where he was a colleague of Roger Adams, Speed Marvel, David Y. Curtin, Nelson J. Leonard, and Reynold C. Fuson.

He is responsible for the hexafluorocumyl alcohol derived "Martin" bidentate ligand and a tridentate analog.

With his doctoral student Daniel Benjamin Dess, he invented the Dess–Martin periodinane that is used for selective oxidation of alcohols.

His later work included studies of the hexaiodobenzene dication that indicated σ-delocalization ("aromaticity") between the iodine atoms.

J.C. Martin received much recognition during his career, including Senior Research Prize from the Alexander von Humboldt Foundation and a Guggenheim Fellowship.