Colloidal core/shell quantum dots (QDs) with environment-friendly feature and controllable optoelectronic properties are promising building blocks in emerging solar technologies. In this work, we rationally design and tailor the eco-friendly CuInSe (CISe)/ZnSe core/shell QDs by Mn doping and stoichiometric optimization (i.e., molar ratios of Cu/In). It is demonstrated that Mn doping in In-rich CISe/ZnSe core/shell QDs can effectively engineer the charge kinetics inside the QDs, enabling efficient photogenerated electrons transfer into the shell for retarded charge recombination. As a result, a solar-driven photoelectrochemical (PEC) device fabricated using the optimized Mn-doped In-rich CISe/ZnSe core/shell QDs (Cu/In ratio of 1/2) exhibits improved charge extraction and injection, showing a ~ 3.5-fold higher photocurrent density than that of the pristine CISe/ZnSe core/shell QDs under 1 sun AM 1.5G illumination. The findings indicate that transition metal doping in “green” nonstoichiometric core/shell QDs may offer a new strategy for achieving high-efficiency solar energy conversion applications.