In this study, the mechanism of chlorinated by‐products (CBPs) formation and transformation during urine electrolysis was comparatively investigated with active and nonactive electrodes. It was found that nutrients removal and CBPs formation was dominated by the chlorine evolution on the active Ti/RuOx‐IrOx electrodes. CBPs formation was inhibited by the ammonia and urea chlorination and kept at a relatively low level before chlorination breakpoint. After the concentration of organic CBPs (OCBPs) increasingly reaching the maximum as a result of the peak concentration of free chlorine, most free chlorine transformed into inorganic chlorination by‐products (ICBPs) with the chlorate as the main species. In contrast, the formation of CBPs on boron‐doped diamond (BDD) electrodes was jointly dominated by the direct oxidation and chlorine mediated oxidation, which resulted in the complete degradation of OCBPs and the accumulation of ICBPs throughout the electrolysis. The organics with high molecular weight readily formed CBPs. Moreover, higher current density would accelerate the production of ICBPs on both electrodes, although it could mitigate OCBPs production at chlorination breakpoint for Ti/RuOx‐IrOx anodes. Separation of chloride ions and organics with high molecular weight from urine using nanofiltration was proposed to mitigate the production of CBPs.