Ecological compensation is a powerful environmental economic tool for environmental protection in areas where drinking water sources are located. We established an ecological compensation accounting system based on respondents’ willingness to accept (WTA). In this system, stakeholder preferences and the factors that influence them can be gauged effectively using logit and tobit models. We applied this accounting system to ecological compensation for the Miyun Reservoir, Beijing, China. The average WTA value for Miyun Reservoir residents was approximately 1186 CNY per family in 2012, which could be set as a suitable compensation standard, since it is slightly higher than the local protection cost. Thus, the annual total ecological compensation could be 58.73 million CNY. Distance from the reservoir, job types, and attitude to environmental protection were variables with significant effects on WTA. In addition, trends for individual preferences were identified via an analysis of key influential factors. The results suggest some useful information for establishing ecological compensation mechanisms for conservation of drinking water sources. Suggestions include popularizing the concept and meaning of ecological compensation among residents, setting different compensation levels based on distance from the reservoir, considering the requirements of farmers, and taking various in-kind and out-of-kind compensation approaches.