Ultraviolet/persulfate (UV/PS) and Ultraviolet/hydrogen peroxide (UV/H2O2) have attracted much attention in recent years as advanced oxidation processes for water treatment. However, it is not all clear how these two methods affect the formation of cyanogen chloride (CNCl) in the subsequent water chlorination process. In this study, it was found that both UV/H2O2 and UV/PS pre-oxidation promoted the formation of CNCl in six actual water samples collected from urban rivers. Glycine, uric acid, arginine and histidine were investigated as the model compounds to explore the effects of different methods on the production of CNCl. The results showed that compared with chlorination alone, pre-oxidation by UV/H2O2 and UV/PS can reduce the production of CNCl for glycine and uric acid by up to 95% during post-chlorination process. However, they can greatly promote the formation of CNCl for arginine and histidine by up to 120-fold. In a more detailed investigation, pre-oxidation of histidine formed highly reactive intermediates to chlorine, leading to increased CNCl formation and chlorine consumption. The results showed that the precursors of CNCl was altered after pre-oxidation, and need to be re-evaluated.