Objective: To investigate risk factors and the nature of the outbreak of bacillary dysentery in Lhasa City, so as to customize targeted prevention and control measures. Methods: Using on site epidemiological investigation, the suspected, probable and confirmed cases of bacillary dysentery in one school and one kindergarten in Lhasa City from June 26 to July 1, 2022 were collected, and additional cases were identified through interview from school staffs and family members, reviewing morning examination records and tracking records of school illness related absence. A case control study was conducted to investigate suspicious meals and drinking raw water, and polymerase chain reaction (PCR) was performed to detect Shigella line nucleic acid fragment in the patients feces, anal swabs, retained food, and terminal water. Results: A total of 55 cases were found in two schools, with the prevalence rate of 15.41% in total and 16.71% in students ( n =53), 7.5% in staff ( n =2). The epidemic curve was suggestive of a point source exposure. The prevalence rate among students who walk to school and students who live in the school showed no difference (16.10%，17.09%)( χ 2=0.05, P >0.05), and the prevalence rate was higher among elementary school students than kindergarten students (19.83%，6.67%)( χ 2=7.13, P <0.05). Case control comparisons showed a direct association between drinking raw water and morbidity in the case and control groups during June 24-26 ( OR=4.01, 95%CI =1.75-9.19, P < 0.05). A total of 23 fecal Shigella nucleic acid positives were detected from the two schools, two from the end water in front of the cafeteria door, and two from sludge in the sewage pipe around the wellhead. Conclusions The outbreak of bacillary dysentery is caused by the contamination of the pipe network water. Health administrative departments should improve the supervision and management of drinking water health safety, and schools should strengthen the management of water supply facilities for effectively prevent of waterborne infectious disease outbreaks.