In this study, biochar-based Fe and Co homonuclear (DAC−Fe−Co) and heteronuclear (DAC-Fe/Co) diatomic catalysts were first prepared via controlling the ligands of Fe and Co, and used to activate peroxymonosulfate (PMS) for the degradation of emerging organic pollutants, such as sulfamethoxazole (SMX), bisphenol A, phenol, atrazine, and nitrobenzene. The results showed that acid pretreatment of biochar was necessary for biochar to synthesize atomic catalysts. The DAC-Fe/Co had higher contents of Fe and Co than DAC−Fe−Co, but lower catalytic activity, in which the SMX first-order kinetics rate constant for DAC−Fe−Co was 4.1 times higher than that for DAC-Fe/Co, achieving 0.32 min −1 . DAC−Fe−Co and DAC-Fe/Co could activate PMS to produce similar reactive species, including radicals and nonradicals. But DAC−Fe−Co produced a higher concentration of radicals than DAC-Fe/Co. The density functional theory (DFT) calculation indicated that compared to DAC-Fe/Co, DAC−Fe−Co had a higher adsorption capacity for PMS (−7.90 eV) and lower energy barrier for the regeneration of Fe (−1.20 eV) and Co (−1.16 eV) active sites. The enhanced regeneration of Fe and Co active sites promoted the formation of radicals, which explained the faster SMX removal rate in the system of DAC−Fe−Co/PMS than DAC-Fe/Co/PMS. The DAC−Fe−Co/PMS system exhibited high resistance to inorganic anions and showed excellent catalytic stability in the cycling experiments. This study provides insight into the discrepant catalytic activity of homonuclear and heteronuclear diatomic catalysts for PMS activation to degrade emerging organic contaminants, and offers a new way to prepare the homonuclear diatomic catalyst.