Rural water supply system is affected by geographical conditions, water resources endowment and regional differences in economic development level. In some areas, rural water supply projects exhibit weak resilience to risks, potentially leading to water shortage or contamination during emergencies. In this paper, the natural disaster risk theory is introduced into the analysis of rural water supply risk. An evaluation index system and the corresponding evaluation model were constructed from four aspects: disaster-causing factors, disaster-prone environment, disaster-bearing entities, and disaster prevention and mitigation capability. Based on data of rural water supply projects in 34 districts in Chongqing in 2020, the rural water supply risk at district level was assessed. According to the calculation results, the risk level was divided into three levels: low, medium and high, with the thresholds set at 0.336 6 and 0.558 1 respectively. Results indicate that five districts (Yongchuan, Beibei, Wansheng, Fengjie and Fuling), primarily located in the urban area, exhibited low risk. Two districts (Wushan and Youyang) were classified as high risk. Wushan is situated in the Three Gorges reservoir area in northeast Chongqing, while Youyang is in the Wuling Mountainous area in southeast Chongqing. The remaining 27 districts were categorized as medium risk. The risk assessment results offer technical support for early warning and response for rural water supply risks in Chongqing.