Reclaimed water as an alternative water source for domestic, industrial, and agricultural purposes is efficient to alleviate the shortage of water resources, so the research and application of reclaimed water is popular in many areas of the world. The process of disinfection is necessary to minimize the public risks associated with exposure to reclaimed water. The target bacteria used in this research were E. coli DH5a, E. coli ATCC 15597, Shigella dysenteriae CGMCC 1.2428, Salmonella typhimurium ATCC 14028, Bacillus subtilis ATCC6633, and three indigenous bacteria total bacteria count (TBC), heterotrophic bacteria (HPC) and total coliform (TC). The principal objectives of this research were to study effects of water quality on UV inactivation，and disinfection efficiency, Synergistic mechanism, and controlling the formation of THMs and the change of genotoxicity during the sequential use of UV and Cl2 in reclaimed water. (1) Different inactivation curves and UV sensitivity were observed for all of the five selected bacteria under UV irradiation. In these experiments, the effect of Fe, humic acid, kaolin, and activated sludge seeded in PBS on kinetcs of UV inactivation was insignificant. Humic acid enforced the ability of photoreactivation while Fe decreased the extent of photoreactivation. (2) In the process of UV inactivation of TBC, HPC and TC in two reclaimed waters collected from two different wastewater reclamation plants using a membrane bioreactor (W1) and a microfilter (W2) as the main treatment processes, respectively, it was found that UV could inactive bacteria in the two reclaimed waters efficiently. Dissolved matter in two reclaimed waters had no influence on the kinetics of UV inactivation but reduced the ability of photoreactivation. Seeded and indigenous particles influenced UV inactivation by two different methods, so seeded particles could not be used to evaluate effect of indigenous particles on UV inactivation in reclaimed water. (3) The decay of chlorine, inactivation efficiency, the formation of disinfection by-product, and the changes of genotoxicity in chlorination were studied in water samples from two different wastewater reclamation plants. The decay of chlorine could be described by the model of Ct=A1*e-k1*t+A2* e-k2*t. Due to the complexity of the reaction of chlorine and matters in reclaimed water, the relationship of water quality with chlorine decay or inactivation efficiency was difficult to conclude. After chlorination, TTHMs in W2 was higher than that in W1, while IR of W1 increased to much more than 2, indicating its positive genotoxicity. (4) During sequential disinfection of UV and Cl2, a great synergism was observed afer consideration of photoreactivation. Pre-UV irradiation decreased the dose of chlorine used, and so the formation of TTHMs and the increase of genotoxicity in reclaimed water were reduced.