Single atom metal-nitrogen-carbon (M-N-C) nanomaterials are recognized as a class of promising candidates alternatively to natural enzymes, but are still restricted by the limited catalytic activity. Tuning the geometric and electronic configurations of atomic active sites via coexistence of single atoms and atomic clusters provides a good avenue to prepare high-performance M-N-C catalysts. Herein, we report a model Fe-N-C catalyst integrating Fe single atoms with Fe atomic clusters on N-doped porous carbon (denoted as FeAC/FeSA-NC) synthesized by a ligand-mediated strategy that pyrolyzes Fe(II)-phenanthroline complexes assembled zeolitic-imidazolate-frameworks (ZIF-8@Fe-Phen). As expected, the as-prepared FeAC/FeSA-NC catalyst exhibits remarkable oxidase-mimicking activity by activating oxygen into the reactive oxygen species, superoxide radicals (O2−). Density functional theory (DFT) calculations reveal that the coupling of Fe single atoms with Fe clusters contribute to lower activation energy, leading to the enhancement of catalytic activity. As a concept application, the FeAC/FeSA-NC nanozyme is employed for ratiometric fluorescence detection of acetylcholinesterase activity and organophosphorus pesticides (OPs) based on the inhibition effect of thiols on nanozymatic activity. The proposed ratiometric bioassay for OPs determination achieves an excellent linearity over 0.005 to 50 ng mL−1, and a low limit of detection of 1.9 pg mL−1. This work not only provides an effective strategy for rationally design of high-performance nanozymes, but also displays a broad prospect of nanozyme for biochemical sensing applications.