Free chlorine as a primary disinfectant encountered difficulties in inactivating highly chlorine-resistant pathogenic microorganisms without excessive disinfection byproducts (DBPs), so alternatives to chlorine disinfection of drinking water need to be investigated. Ozone and ultraviolet have the potential for application in the disinfection of drinking water, due to high bactericidal capability. In this work, inactivation of typical pathogenic microorganisms such as rotavirus and Bacillus subtilis spores by sequential ozone/cholrine and UV/chlorine disinfection was evaluated in raw water. Moreover, the disinfection efficiency, synergy mechanism and impact factors of disinfection effect during sequential disinfection were also investigated. The main research results are shown as follows: (1) As indicator microorganisms, the inactivation of Bacillus subtilis spores with sequential disinfection with ozone followed by free chlorine was investigated. Ozone pretreatment disrupts surface layer and outer spore coat, reduces chlorine-resistant of spores, resulting in enhancing disinfection efficiency of chlorine for Bacillus subtilis spores. Inactivation rate of spores with chlorine increase and consumption of chlorine decrease according to the level of preozonation. (2) Inactivation of enteropathogenic microorganisms by UV exposure was investigated in collimated beam tests. The inactivation kinetics of Escherichia coli, Shigella dysentery, Wa strain rotavirus by UV can be described with first-order kinetics. Salmonella typhimurium was characterized by a lag phase, followed by a pseudo-first-order and tailing of inactivation. Due to the similaration of inactivation kinetics by UV in drinking water and phosphate-buffered saline (PBS), the experiment results obtained in PBS can be applied to drinking water. (3) The photoreactivation of Shigella dysentery, Salmonella typhimurium, Escherichia coli under irradiation of fluorescent lamps after UV disinfection was investigated. Results show that photoreactivation rate of bacteria is influenced by the UV radiation dose as well as their UV–resistance. With the increasing of UV resistance of bacteria, it requires higer UV dose to inhibit photoreactivation completely. Fulvic acid in water is conductive to bacterial photoreactivation. Photoreactivation rate increases with increasing doses of UV radiation for fulvic acid. (4) Due to the problem of photoreactivation of bacteria, Squential inactivation of bacteria with UV/chlorine was studied. Compared with chlorine disinfection individual, consumption of chlorine residuals decreases in sequential UV/chlorine disinfection. Lower concentration of chlorine can restrain bacterial photoreactivation, leading to inhibit the production of DBPs.