Copper indium selenide (CISe) is a prototype infrared semiconductor with low toxicity and unique optical characteristics. Its quantum dots (QDs) accommodate ample intrinsic point defects which may actively participate in their rather complex photophysical processes. We synthesize CISe QDs with similar sizes but with distinct highly stoichiometry-deviating atomic ratios. The synthesis condition employing Se-rich precursors yields the Cu-deficient CISe QDs with special photophysical properties. The photoluminescence exhibits monotonic red shift from 680 to 775 nm when the ratio of Cu’s proportion to In’s decreases. The luminescence is found to stem from the copper vacancy and antisite defects. The CISe QDs exhibit Raman activity at 5.6, 6.9, and 8.7 THz that is separately assigned to Cu–Se and In–Se optical phonon modes and surface mode.