In order to further promote the implementation of the River Chief System and enhance the effectiveness of water environment management in the Yangtze River Basin, the framework of integrated theory is summarized. The compatibility between the integrated theory and the River Chief System is explored. The general situation of the implementation of the River Chief System in the Yangtze River Basin is reviewed. The problems in the implementation of the River Chief System are analyzed from the perspective of governance of the integrated theory, such as the simplification of the participants in the governance, the separation of public interest departments, the fragmentation of integration at the same level and the high dependence on authoritative organizations. Finally, some suggestions are put forward for improving the reform of the River Chief System in the Yangtze River Basin as follows: encouragement of participation of multiple organizations, promotion of incentive and restraint mechanism, improvement of integrated mechanism at the same level, and establishment of networked information management systems for the government.