In river basins that cross jurisdictional boundaries, water quality degradation has become a crucial problem and results in intensive competition among water users, especially in developing countries. Under this situation, implementing water quality management and control across jurisdictional boundaries can strengthen watershed pollution controls, and prevent pollution from being passed on and promote active pollution control within the related jurisdictional regions. This study examined the limitations of the current trans-boundary water quality management system in China and reviewed the planning and implementation of two pilot integrated trans-boundary water management systems established in the Jiangsu and Zhejiang provinces. Based on our findings, we proposed a new policy framework for trans-boundary water quality management. As a first step toward integrated watershed management in China, this policy framework can help assess the actual water pollution status of various regions and serve as a basis for an integrated watershed management system. The framework can be easily applied in other countries with trans-boundary water pollution issues, particularly in the context of developing countries.