Electrosynthesis of hydrogen peroxide through the two-electron oxygen reduction pathway provides a crucial alternative to the energy-intensive anthraquinone process. Nevertheless, the efficicency for hydrogen peroxide generation is limited by the competitive four-electron pathway. In this work, we report a noncovalent modulation strategy for the isolated CoN₄ sites by metal-phthalocyanine molecules confinement, which boosts the two-electron oxygen reduction towards generating hydrogen peroxide. The confined Co-phthalocyanine molecules on CoN₄ sites through π–π interactions induce the competitive *OOH adsorption between the two Co sites formed nanochannel. This noncovalent modulation contributes to the weakened *OOH binding on CoN₄ sites and thus suppresses its further dissociation, achieving the maximum selectivity of 95% with high activity for H₂O₂ production. This work shows that tailoring noncovalent interactions beyond the binding sites is a promising approach to modulate the local structure of isolated metal sites and related catalytic performance.