Messier specialized on comet hunting, and observed 44 of them during his professional life (plus at least one - the great comet of 1744, described by De Chéseaux - which he had observed from Lorraine in young years). Of these he had originally discovered 13, and independently co-discovered another 7.

His most important work, however, was the compilation of his Catalog of Nebulae and Clusters of Stars, which he created in order to list those nebulous objects which might be easily confused with comets, in the telescopes of his days. The final published version of the catalog contained 103 entries, but the modern version of this list has been extended to 110 objects, the seven additional objects added from notes of Charles Messier and Pierre Méchain, who at that time collaborated with him. Of these deepsky objects, Messier originally discovered 39 or 40, and independently re- (or co-) discovered at least 10; Pierre Méchain originally discovered 29 and co-discovered 1 of the objects in Messier's catalog.

Charles Messier has been honorerd by naming a moon crater after him; moon crater Messier (1.9S, 47.6E, 11.0 km diameter) was officially named in 1935. In 1996, asteroid 7359, discovered on January 16, 1996 by M. Tichy at Klet Observatory, and provisionally designated 1996 BH, was named "Messier"; it had already been observed previously, and designated 1978 WR14 and 1989 WT1. The proposition of Lalande to name a constellation after him, Custos Messium, has been a short episode only; Custos is longly extinct.