To establish a sound ecological compensation (EC) mechanism in the Xin’an River Basin, this study suggested utilizing ecosystem service valuation to determine the compensation amount. In this study, the first step was to establish a reasonable watershed EC model using the ecological compensation supply coefficient (ECSC) based on the value spillover theory (VST) of the ecosystem services and the ecological compensation demand coefficient (ECDC). The second step was to classify the ecosystem services of the Xin’an River Basin into three categories, including supply service, regulating service, and cultural service, with 14 specific functions to determine the ecological compensation standard accounting scope in these services. Then, a case study on the Xin’an River Basin for EC standards was presented. The total ecosystem service value (ESV) in the Xin’an River Basin was estimated to be CNY 70.271 billion, with supply service accounting for 22.7%, regulating service accounting for 24.6%, and cultural service accounting for 52.7%. Based on the compensation scope, the ecosystem service values for the upper and lower limits of the EC were calculated as CNY 57.779 billion and CNY 17.292 billion. Combined with the results of the ECSC and ECDC, the upper and lower limits of the EC standard in the Xin’an River Basin were computed to be CNY 4.085 billion and CNY 1.438 billion, respectively. Therefore, the ESV-based EC model for the Xin’an River Basin can effectively address the challenge of inadequate EC in the watershed. It also facilitates balanced regional development and serves as a theoretical foundation and empirical evidence for the government to establish a unified national policy on cross-border river basin ecological compensation.