Abstract Artificial photosynthesis emerges as a strategic pathway to produce hydrogen peroxide (H 2 O 2 ), an environmentally benign oxidant and a clean energy carrier. Nonetheless, in many heterojunction‐based artificial photosynthetic systems, the H 2 O 2 productivity is significantly hindered by poor carrier transport, narrow spectral light absorption, and a lack of adequate active sites for the two‐electron oxygen reduction reaction. Herein, a catalyst architecture with an iso‐elemental heterojunction formed by interfacing Zn 3 In 2 S 6 nano‐flowers and ZnIn 2 S 4 nanosheets is proposed. This catalyst exhibits a H 2 O 2 production rate as high as 23.47 µmol g −1 min −1 under UV–vis light irradiation, which is attributed to the minimized contact energy barrier and enhanced lattice match at the ZnIn 2 S 4 /Zn 3 In 2 S 6 interface thanks to the iso‐elemental catalyst architecture which aids in enhanced efficient separation and transfer of photogenerated carriers. Theoretical simulations alongside comprehensive in‐situ and ex‐situ characterizations confirm the photo‐redox sites for H 2 O 2 generation and effective carrier dynamics across the catalyst surface. Moreover, substituting one reduction‐type catalyst ZnIn 2 S 4 with other non‐iso‐elemental catalysts like CdIn 2 S 4 , TiO 2 , and CdS further confirms the feasibility and superiority of the proposed iso‐elemental configuration. This work offers a new perspective on designing heterojunction catalysts for artificial photosynthesis of H 2 O 2 .