UV/chlorine process, as an emerging advanced oxidation process (AOP), was effective for removing micro-pollutants via various reactive radicals, but it also led to the changes of natural organic matter (NOM) and formation of disinfection byproducts (DBPs). By using negative ion electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS), the transformation of Suwannee River NOM (SRNOM) and the formation of chlorinated DBPs (Cl-DBPs) in the UV/chlorine AOP and subsequent post-chlorination were tracked and compared with dark chlorination. In comparison to dark chlorination, the involvement of ClO•, Cl•, and HO• in the UV/chlorine AOP promoted the transformation of NOM by removing the compounds owning higher aromaticity (AImod) value and DBE (double-bond equivalence)/C ratio and causing the decrease in the proportion of aromatic compounds. Meanwhile, more compounds which contained only C, H, O, N atoms (CHON) were observed after the UV/chlorine AOP compared with dark chlorination via photolysis of organic chloramines or radical reactions. A total of 833 compounds contained C, H, O, Cl atoms (CHOCl) were observed after the UV/chlorine AOP, higher than 789 CHOCl compounds in dark chlorination, and one-chlorine-containing components were the dominant species. The different products from chlorine substitution reactions (SR) and addition reactions (AR) suggested that SR often occurred in the precursors owning higher H/C ratio and AR often occurred in the precursors owning higher aromaticity. Post-chlorination further caused the cleavages of NOM structures into small molecular weight compounds, removed CHON compounds and enhanced the formation of Cl-DBPs. The results provide information about NOM transformation and Cl-DBPs formation at molecular levels in the UV/chlorine AOP.