Semiconductor quantum dots (QDs) in conjunction with non-noble 3d-metal ions (e.g., Fe3+, Co2+, and Ni2+) have emerged as an extremely efficient, facile, and cost-effective means of solar-driven hydrogen (H2) evolution. However, the exact structural change of the active sites under realistic conditions remains elusive, and the mechanism of H2 evolution behind the remarkable activity is poorly understood. Here, we successfully track the structural variation of the catalytic sites in the typical H2 photogeneration system consisting of CdSe/CdS QDs and 3d-metal ions (i.e., Ni2+ used here). That is, the nickel precursor of Ni(OAc)2 changes to Ni(H2O)62+ in neutral H2O and eventually transforms to Ni(OH)2 nanosheets in alkaline media. Furthermore, the in operando spectroscopic techniques of electron paramagnetic resonance and X-ray absorption spectroscopy reveal the photoinduced transformation of Ni(OH)2 to a defective structure [Nix0/Ni1-x(OH)2], which acts as the real catalytic species of H2 photogeneration. Density functional theory (DFT) calculations further indicate that the surface Ni-vacancies (VNi) on the Ni(OH)2 nanosheets enhance the adsorption and dissociation of H2O molecules to enhance the local proton concentration, while the Ni0 clusters behave as H2-evolution sites, thereby synergistically promoting the activity of H2 photogeneration in alkaline media.