The contingent valuation method is used to study the service value regarding the water resources reservation of the South-to-North Water Diversion Project in Beijing. The analysis results illustrate that the mean willingness to pay (WTP) is 42.15 CNY per permanent resident of Beijing. We propose a WTP analysis model based on the Bayesian network for its obvious advantages compared to previous models. The results demonstrate certain factors crucial to WTP, including “public support for the project expenditure of financial, material, and human resources to reserve water resources”, “willingness to participate in public benefit activities”, “public cognition of water scarcity in Beijing”, “monthly family income”, and “knowledge of the project”. This study concentrates on the variables that are of most concern to the government, including “education background”, “occupation”, “public cognition of water scarcity in Beijing”, and “public awareness of the SNWDP”. The future of China’s environmental strategy will gradually be market-oriented, and this study also provides a basis for the government to gain insight into public payment behaviour impact factors and set policies.