Biochar has the issues with inadequate stability and low catalytic activity. In this study, two-step ball milling method was applied to synthesis carbon nitride co-modified cyanobacteria biochar (CN-BC). The optimized CN-BC can effectively activate peroxymonosulfate (PMS) to degrade emerging pollutants. The degradation rate constant of enrofloxacin in the CN-BC/PMS system reached 0.506 min−1, and 95 % of enrofloxacin could be effectively degraded within 10 min. Free radical quenching experiments and electrochemical experiments confirmed that the electron transfer and 1O2 were the main pathways in the CN-BC/PMS system. The CN-BC/PMS system has selective degradation of electron-rich pollutants, and the pollutants containing electron-donating groups are more easily degraded than those containing electron-withdrawing group. The selective degradation pathway of pollutants by CN-BC was further analyzed using density functional theory (DFT). Continuous flow CN-BC/PMS membrane system showed long-term abatement of emerging pollutants. This study improves the understanding of the mechanism of PMS activation by cyanobacterial biochar catalysts and provides a new pathway for membrane-based domain-limited catalysis.