The trans-regional characteristics of watershed governance produce more problems beyond the capacity of each individual water-related department, leading to the fragmentation of watershed management. The River Chief System (RCS) has experienced swift developments over the past decade in China by appointing the local government heads as river chiefs. RCS works efficiently in the short-term due to its superiority in the inclusion of clear responsibility, authority, and multi-sectoral collaboration. However, the characteristics of the authority-based vertical coordination of the hierarchical system remain unchanged, and therefore the problems of organizational logic and the responsibility dilemma still exist. Tasks including perfecting of laws, integrated watershed management, and public participation still need to be completed. RCS reflects the routine and characteristics of the migration of national governance, and as such provides new insights for other developing countries in the design of river management systems.