Peroxymonosulfate (PMS) is receiving increasing interest as an oxidant used during the disinfection of drinking water. However, it does not have continuous disinfection ability as sodium hypochlorite (NaClO) does. PMS/Cl- can produce reactive chlorine species and thus provide a persistent disinfectant residual in distribution systems. This study investigated PMS/Cl- disinfection versus NaClO disinfection in terms of the formation and estimated cytotoxicity of CX3R-type disinfection by-products (DBPs) under the same dose of free chorine. Results showed that free chlorine produced by PMS/Cl- reaction can react with organic compounds and the productions of CX3R-type DBPs were dependent on the free chlorine dose, pH and reaction time. Specifically, chloroform (CF) and chloral hydrate (CH) generally increased with increasing of free chlorine dose and reaction time. CF increased steadily with increasing pH, while CH firstly increased and then decreased with increasing pH. Haloacetonitriles and haloacetamides firstly increased and then decreased with increasing of free chlorine dose and reaction time, and decreased continuously with increasing pH. The formation pathway of CX3R-type DBPs during chlorination (PMS/Cl-) of tyrosine was proposed, based on the detected intermediates (i.e., Benzyl cyanide, 4-hydroxy-benzyl-cyanide, 4-chlorophenol, 2,4-dichlorophenol, and 2,4,6-trichlorophenol). The estimated cytotoxicity of CX3R-type DBPs in chlorinated water firstly increased and then decreased with the increasing of reaction time, free chlorine dose and pH, which highly related to the changes of DCAN (the most toxic CX3R-type DBP) levels. Comparing to NaClO disinfection, PMS/Cl- disinfection can better control the formation and cytotoxicity of CX3R-type DBPs, which was attributed to the degradation of natural organic matter, CX3R-type DBPs intermediates and CX3R-type DBPs by the residual PMS. This study demonstrated the superiority of PMS/Cl- as an alternative disinfectant comparing to NaClO.