AbstractPathogenic bacteria are the main cause of bacterial infectious diseases, which have posed a grave threat to public health. Single‐atom nanozymes have emerged as promising candidates for antibacterial applications, but their activities need to be further improved. Considering diatomic nanozymes exhibit superior metal loading capacities and enhanced catalytic performance, a new interlayer coupling diatomic nanozyme (IC‐DAN) is constructed by modulating the coordination environment in an atomic‐level engineering. It is well demonstrated that IC‐DAN exhibited superior peroxidase‐mimetic activity in the presence of H2O2 to yield abundant ∙OH and possessed high photothermal conversion ability, which synergistically achieves efficient antibacterial therapy. Therefore, IC‐DAN shows great potential used as antibacterial agent in clinic and this study open a new route to developing high‐performance artificial enzymes.