Abstract: Constructing inter-basin water transfer ecological compensation mechanism for inter-basin water transfer is one of the effective ways to adjust the interest relationship and promote sustainable development in the region. Public’s willingness is an important basis for establishing the ecological compensation mechanism of the inter-basin water transfer. Based on theoretical exploration, field investigation and model analysis, the willingness to pay（WTP） value and influencing factors of ecological compensation of inter-basin water transfer project are analyzed in Jinnan, Shandong Province, the water-receiving area of the eastern route of the South-to-North Water Transfer Project. The WTP value is 206.29 RMB/（person·year） obtained through the combination of non-parametric and parametric methods. Bayesian network model is employed to explore the influencing factors, it is found that educational background, per capita monthly household income, the recognition of the importance of the project to the city or the country and whether the project has a positive impact on your life have the greater influence on WTP. Then, SWOT matrix analysis method is adopted to put forward incentive mechanism from the perspectives of internal public background and external environmental policies.This study is to provide reference for the construction of ecological compensation mechanism of inter-basin water transfer project, and to put forward countermeasures and suggestions for social capital to participate in water conservancy construction management.