Magnetic configurations critically influence the electronic structure and catalytic behavior of M–N–C single-metal atom catalysts (SACs). Here, we computationally establish a strong correlation between spin state transitions and the tuning of out-of-plane geometric displacement, which can be utilized to improve the activity of the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) across 3d, 4d, and 5d transition metals. Out-of-plane displacement coupled with oxidative adsorption generally lowers orbital splitting, favoring high-spin states for 3d elements and in turn strengthens the adsorption of reaction intermediates. SACs can be classified into three categories, preferring large, medium, and small displacements based on their d-electron count, with medium displacement leading to spin crossover. We show that this tuning can reduce the ORR overpotentials by 0.42 V (Mn–N–C), 0.37 V (Fe–N–C), and 0.13 V (Co–N–C), and the OER overpotentials by 0.20 V (Mn–N–C), 0.49 V (Fe–N–C), 0.10 V (Co–N–C), and 0.28 V (Ni–N–C). Stability analysis with hybrid Pourbaix diagrams revealed challenges in acidic or oxidative environments. While the proposed scheme is experimentally challenging, our study provides a systematic theoretical framework for enhanced spin-engineered M–N–C SACs based on modified local structure.