To strengthen the overall planning and coordination of river basins and improve the level of joint management and great protection of rivers and lakes are problems to be solved in implementing the river chief system. By summarizing the progresses of river chief system and analyzing the demand for overall planning, we put forward suggestions on enhancing the capacity of overall planning and coordination for major river basins as follows: (1) the current water related management law can be revised, the legislation of large rivers and lakes protection promoted; regulation for river basin protection and guidance for joint prevention and control should be promulgated for trans-provincial rivers and lakes. (2) Inter-ministerial cooperation should be deepened through the inter-ministerial joint meeting platform, and basin cooperation should be facilitated by establishing and improving the “basin management organization in association with provincial river chief office”; regional cooperation can be fostered by employing and assigning personnel among provincial river chief offices in the basin. (3) A unified planning, unified standard and joint implementation mechanism can be built throughout the basin. (4) The inter-ministerial joint meeting office should supervise and inspect the overall planning of major river basins, and the investigation results can be taken as annual comprehensive evaluation basis for provincial leaders. (5) Inter-ministerial cooperation can be carried out for watershed monitoring and information sharing; water-related big data center can be built by basin management organizations; joint monitoring of provincial boundaries can be conducted between provincial river chief offices of adjacent provinces. (6) Ecological compensation should be regraded as the key issue of inter-ministerial cooperation, and basin management organizations should participate in ecological management.