The anchoring sites of metal single atoms are closely related to photogenerated carrier dynamics and surface reactions. Achieving smooth photogenerated charge transfer through precise design of single-atom anchoring sites is an effective strategy to enhance the activity of photocatalytic hydrogen evolution. In this study, Pt single atoms were loaded onto ultra-thin carbon nitride with two-coordination nitrogen vacancies (VN2c-UCN-Pt) and ultra-thin carbon nitride with three-coordination nitrogen vacancies (VN3c-UCN-Pt). This paper investigated the photocatalytic hydrogen evolution performance and photogenerated carrier behavior of Pt single atoms at different anchoring sites. Surface photovoltage measurements indicated that VN2c-UCN-Pt exhibits a superior carrier separation efficiency compared to VN3c-UCN-Pt. More importantly, the surface photovoltage signal under the presence of H2O molecules revealed a significant decrease. Theoretical calculations suggest that VN2c-UCN-Pt exhibits superior capabilities in adsorbing and activating H2O molecules. Consequently, the photocatalytic hydrogen evolution efficiency of VN2c-UCN-Pt reaches 1774 µmol g−1h−1, which is 1.8 times that of VN3c-UCN-Pt with the same Pt loading. This work emphasized the structure–activity relationship between single-atom anchoring sites and photocatalytic activity, providing a new perspective for designing precisely dispersed single-atom sites to achieve efficient photocatalytic hydrogen evolution.