Atomically precise Cu clusters are highly desirable as catalysts for CO2 reduction reaction (CO2RR), and they provide an appropriate model platform for elaborating their structure–activity relationship. However, an efficient overall photocatalytic CO2RR with H2O using assembled Cu-cluster aggregates as heterogeneous photosensitive semiconductors has not been reported. Herein, we report a stable crystalline Cu–S–N cluster photocatalyst with local protonated N–H groups (denoted as Cu6–NH). The catalyst exhibits suitable photocatalytic redox potentials, high structural stability, active catalytic species, and a narrow bandgap, which account for its outstanding photocatalytic CO2RR performance under visible light, with ~100% selectivity for CO evolution. Remarkably, systematic isostructural Cu-cluster control experiments, in situ infrared spectroscopy, and density functional theory calculations revealed that the protonated pyrimidine N atoms in the Cu6–NH cluster act as a proton relay station, providing a local proton during the photocatalytic CO2RR. This efficiently lowers the energy barrier for the formation of the *COOH intermediate, which is the rate-limiting step, efficiently enhancing the photocatalytic performance. This work lays the foundation for the development of atomically precise metal-cluster-based photocatalysts.