Herein, we engineered the cobalt core size and carbon shell thickness of Co@C by molten salt electrolysis (MSE) to investigate the enhanced essence of decreasing core size as well as the shell thickness dependence-mediated transition of catalytic mechanisms. We found that the reaction activation energy (RAE) of Co@C/peroxymonosulfate (PMS) systems was intimately dependent on the core sizes for sulfamethoxazole (SMX) degradation. The smaller core size of 26 nm provided a lower RAE of 13.39 kJ mol−1. In addition, increasing carbon shell thicknesses of Co@C altered the catalytic mechanisms from a radical pathway of SO4•– and •OH to to a non-radical pathway of 1O2 and electron-transfer process (ETP), which were verified by experimental results and density functional theory (DFT) calculations. Interestingly, increasing carbon shell thicknesses promoted the charge transfer between Co metal slab and carbon shell, increased the adsorption energy of PMS molecule on the Co@C slab, and decreased the length of OO, which favoured the occurrence of non-free radical processes.