Abstract Most previous efforts have concentrated on extrinsic structural modification to elucidate the catalytic behavior of metal oxide nanozymes, while the influence of intrinsic metal–oxygen (M–O) bonding properties remains underexplored. Herein, we report an ion-intercalation strategy to tailor the Mn–O covalency in layered Birnessite. The polarization effect induced by intercalated alkaline-earth ions (Mg2+, Ca2+, Sr2+, Ba2+) strengthens the Mn–O bond. This effect synergistically optimizes the electronic structure of both Mn and O sites, evident from the accumulated electron density and upshifted band centers. This enhancement endows the nanozyme with a superior oxidase-like activity, featuring a higher specific activity, improved substrate affinity, and accelerated reaction kinetics. Mechanistic studies reveal that the strengthened covalency facilitates substrate adsorption, promotes electron transfer and O–O bond dissociation, and lowers the energy barrier for the rate-determining step. Leveraging this performance, a colorimetric sensor array was constructed for the precise identification of five antioxidants (TA, AA, EGC, GA, CYS). This work elucidates the pivotal role of metal–oxygen covalency in catalysis and establishes a novel paradigm for the electronic-structure engineering of high-performance nanozymes.