Heavy‐metal‐free ternary Cu–In–Se quantum dots (CISe QDs) are promising for solar fuel production because of their low toxicity, tunable band gap, and high light absorption coefficient. Although defects significantly affect the photophysical properties of QDs, the influence on photoelectrochemical hydrogen production is not well understood. Herein, we present the defect engineering of CISe QDs for efficient solar‐energy conversion. Lewis acid–base reactions between metal halide–oleylamine complexes and oleylammonium selenocarbamate are modulated to achieve CISe QDs with the controlled amount of Cu vacancies without changing their morphology. Among them, CISe QDs with In/Cu = 1.55 show the most outstanding photoelectrochemical hydrogen generation with excellent photocurrent density of up to 10.7 mA cm−2 (at 0.6 VRHE), attributed to the suitable electronic band structures and enhanced carrier concentrations/lifetimes of the QDs. The proposed method, which can effectively control the defects in heavy‐metal‐free ternary QDs, offers a deeper understanding of the effects of the defects and provides a practical approach to enhance photoelectrochemical hydrogen generation.