We have synthesized highly luminescent Cu-In-S nanocrystals by heating the mixture of metal carboxylates and alkylthiol under inert atmosphere. We modified the surface of CIS nanocrystals with zinc carboxylate and subsequent injection of alkylthiol. As a result of the surface modification, highly luminescent CIS@ZnS core/shell nanocrystals were synthesized. The luminescence quantum yield (QY) of best CIS@ZnS nanocrystals was above 50%, which is more than 10 times higher than the initial QY of CIS nanocrystals before surface modification (QY = 3%). Detailed study on the luminescence mechanism implies that etching of the surface of nanocrystals by dissociated carboxylate group (CH3COO-) and formation of epitaxial shell by Zn with sulfur from alkylthiol efficiently removed the surface defects which are major non-radiative recombination sites in semiconductor nanocrystals. In this study, we developed a novel surface modification route for monodispersed highly luminescent Cu-In-S nanocrystals with less toxic and highly stable precursors.