Bromate (BrO3−) is a predominant undesired toxic disinfection by-product (DBP) during ozonation of bromide-containing waters. The reduction of BrO3− by zero valent iron (ZVI) and its effect on formation of organic halogenated DBPs during chlorination were investigated in this study. The presence of ZVI could reduce BrO3− to bromide (Br−), and Br− formed could be transformed to free bromine (HOBr/OBr−) during chlorination, further leading to organic brominated (Br-) DBPs formation. Formation of DBPs during chlorination, including trihalomethanes (THMs) and haloacetonitriles (HANs) was detected under different conditions. The results showed that when ZVI dosage increased from 0 to 1 g L−1, the formation of Br-DBPs (e.g., TBM and DBCM) was significantly improved, while the formation of Cl-DBPs (e.g., TCM, TCAN and DCAN) reduced. Higher ZVI dosage exhibited inhibitory effect on Br-DBPs formation due to the competition between ZVI and free chlorine (HOCl/OCl−). The bromine substitution factor (BSF) of THMs significantly decreased from 0.61 ± 0.06 to 0.22 ± 0.02, as the pH was raised from 5.0 to 9.0. Besides, the increase of initial BrO3− concentration significantly improved the formation of Br-DBPs and decreased the formation of Cl-DBPs, leading to an obvious rise on the BSF of THMs. As the initial concentration of HOCl increased, all THMs and HANs gradually increased. Moreover, the analysis based on the cytotoxicity index (CTI) of the determined DBPs showed that reduction of BrO3− by ZVI during chlorination had certain risks in real water sources, which should be paid attention to in the application.