Atom engineering has been demonstrated to be an efficient strategy for optimizing the activities of Prussian blue analogue (PBA)-based nanozymes. Herein, using a series of metal atom-coordinated N PBAs as models, a mechanistic insight into the effect of substituted metal centers on the antioxidant activities of PBA-based nanozymes is provided for the first time. The PBAs exhibit substituted metal atom-dependent antioxidant activities and the optimal Cu-substituted PBAs can effectively protect cells from oxidative stress. Experimental characterization reveals that the effect of low redox potential significantly improves the catalytic antioxidant efficiency. Furthermore, theoretical calculations show that the catalytic activities are well related to the magnetic moment of the adjacent Fe site, which features a linear correlation with the energy barrier of the rate-determining step or adsorption energy of the substrate, respectively. This study may inspire further exploration of PBAs and shed light on the rational design of advanced antioxidant nanozymes.