A simple low-cost and phosphine-free colloidal method was developed to prepare disk-shaped Cu2−xS nanocrystals (NCs) with different crystal structures and basal planes, which could be manipulated effectively by varying the Cu : S feed molar ratios and the amount of surfactants. The near-infrared (NIR) localized surface plasmon resonance (LSPR) wavelength could be tuned from 1133 to 1512 nm with the crystal phase changing from CuS (covellite) to monoclinic Cu7S4 (roxbyite) and Cu31S16 (djurleite). Phase transformation had more important effects on tuning the plasmonic resonance than the surface interaction of the deprotonated carboxyl functional group of oleic acid. Moreover, the crystal phase could transform from covellite to djurleite and the morphology underwent a transition from nanodisks to nanospheres when the post-treatment temperature of CuS nanodisks by dodecanethiol (DDT) was increased to 120 °C, but only a size decrease took place at room temperature. As a result, a slight red-shift of the LSPR wavelength was observed at room temperature, but an obvious red-shift from 1140 to 1910 nm with the change in crystal structure and morphology. The post-treatment temperature played an important role in tuning the plasmonic resonance of the products, which was closely associated with the variation of the crystal structure, morphology and surface properties.