Fine regulation of geometric structures has great promise to acquire specific electronic structures and improve the catalytic performance of single-atom catalysts, yet it remains a challenge. Herein, a novel seed encapsulation–decomposition strategy is proposed for the geometric distortion engineering and thermal atomization of a series of Cu-Nx/S moieties anchored on carbon supports. During pyrolysis, seeds (Cu2+, CuO, or Cu7S4 nanoparticles) confined in metal organic framework can accommodate single Cu atoms with Cu–N or Cu–S coordination bonds and simultaneously induce C–S or C–N bond cleavage in the second coordination shell of Cu centers, which are identified to manipulate the distortion degree of Cu-Nx/S moieties. The severely distorted Cu-N3S molecular structure endows the resultant catalyst with excellent oxygen reduction reaction activity (E1/2 = 0.885 V) and zinc-air battery performance (peak power density of 210 mW·cm−2), outperforming the asymmetrical and symmetrical Cu-N4 structures. A combined experimental and theoretical study reveals that the geometric distortion of Cu-Nx/S moieties creates uneven charge distribution by a unique topological correlation effect, which increases the metal charge and shifts the d-band center toward the Fermi level, thereby optimizing the inter-mediate adsorption energy.