The deterioration of water pollution drainage in China is caused by poor administrative structure as well as natural forces. Low efficiency even inefficiency in trans-jurisdictional water pollution management by local governments, has resulted in environmental accompanying economic development, many conflicts between people living up and-down-stream, and potential hidden trouble in social destabilization. By examining the reform of the water pollution management and cooperation mechanism between Jiangsu and Zhejiang Provinces, this paper tries to illustrate policy evolution process between two provinces, to understand the difficulties in trans-jurisdictional water pollution management of river basins in China. The case study shows the integrated reform of trans-jurisdictional water pollution control based on "Tiao-Kbai-System" that coordinates between central-local government structure and department inner-system should consist of institutions, mechanism and law reforms.