Non-planar nest-like [Fe2S2] cluster sites in N-doped carbon plane with similar active center atomic composition to ferredoxin achieve efficient O2 adsorption and activation while avoiding too robust adsorption of OH* intermediate, thus realizing excellent oxygen reduction reaction (ORR) performance beyond planar [FeN4] and [Fe2N6]. This work provides insights into co-regulation of atomic composition and spatial configuration for efficient ORR catalysis.