Achieving synergy between single atomic site and charge transfer in heterojunction is significant for synthesising photocatalysts with excellent properties. In this paper, single atom Cu/Ta3N5/CdIn2S4 S-scheme hierarchical polyhedrons (SACu/TN/CIS SHPs) have been successfully synthesized by a three-step simple chemistry process. We dive into the improvement of photocatalytic activity in the synergistic effect of SACu and S-scheme. The excellent charge separation and reducing the energy barrier during the ammonium production reaction in the synergistic effect were confirmed by density functional theory (DFT) calculations and physicochemical mechanistic investigations. Electron spin resonance (ESR) corroborated production of reducing agent to accelerate the progress of NO3− to NH3. Under light conditions, the NH3 production rate for SACu/TN/CIS SHPs is an astonishing ∼43.6 times higher than that of original Ta3N5. This report not only recommends an efficient catalyst under visible light, but also proposes an advantageous solution for photocatalytic nitrate reduction in natural conditions.