It is commonly acknowledged that proteins, comprising a large portion of dissolved organic nitrogen pool, are important precursors of disinfection by-products (DBPs). Moreover, proteins can also undergo degradation (e.g. enzymolysis) in aquatic environment or during biological treatment processes. In this study, a well-characterized protein, bovine serum albumin (BSA) was used as model compound to investigate the effect of enzymolysis on the formation of four classes of CX3R-type DBPs (i.e. trihalomethanes, haloacetaldehydes, haloacetonitriles, and haloacetamides) during chlorination. After enzymolysis, the three-dimension structure of BSA was destroyed, increasing the accessibility of inside amino acids to chlorine, thus enzyme-hydrolysed BSA exhibited higher chlorine demand and higher formation of total organic halogen (TOX) than un-hydrolysed BSA. Generally, enzyme-hydrolysed BSA produced more CX3R-type DBPs, which is due to the facilitation of fragmentation of BSA by enzymolysis. In the presence of bromide, enzymolysis promoted the formation of TOX to a greater extent than in the absence of bromide. The effect of enzymolysis on pre-oxidation efficiency in the control of CX3R-type DBPs was also investigated. It was found that the reduction in CX3R-type DBP formation from chlorinated enzyme-hydrolysed BSA was more significant than that from chlorinated un-hydrolysed BSA, but the former still exhibited higher calculated cytotoxicity than the latter, indicating the removal of CX3R-type DBP precursors was indirectly offset by the effect of enzymolysis. This study provides insights into the effect of the structural transformation of protein during water treatment processes on CX3R-type DBP formation.