Ecological compensation is an important means to coordinate the contradiction between environmental protection and regional development fairness. Eastern Lake Taihu is an important source of drinking water for Suzhou, Jiaxing and Shanghai cities. This paper analyzes the connection between water quality protection behavior and loss of development right value in Suzhou city. Based on geographic factor correction, the paper applies regional comparison method to evaluate the loss of development right in drinking water source protection region in eastern Lake Taihu, as the standard of eco-compensation. It shows that the loss of development right in eastern Lake Taihu in 2009 is 4.239 billion yuan, while the loss of local fiscal revenue, farmers' income and urban residents' income accounting for 75.88%, 13.58% and 10.53%, respectively. In order to narrow the income gap between urban and rural residents, farmers should be given priority on the implementation of eco-compensation. The external benefit from water protection behavior has beyond the value of water supply, so overall the eco-compensation police in a greater region is needed.