As an innovative measure of ecological civilization system reform, the river chief system has gradually become a key work in building happy rivers and lakes and helping the high-quality development of water conservancy in the new stage. However, in practice, the implementation effect of the river chief system is not good because of the lack of performance of the functions of the river chief, the lack of collaborative governance mechanism and the low participation of the public. Based on the systematic review and summary of the existing theoretical research and practical experience, this paper discusses the synergistic effect of digital twin technology in the innovation of river chief system management mechanism and possible problems and challenges, and puts forward corresponding countermeasures and suggestions. Digital twin technology can play a synergistic role with the river chief system in professional knowledge, rapid response, collaborative cooperation, public participation and multiple linkage, and provide solutions to the existing problems of the river chief system. In order to establish a digital twin system more suitable for the work of river chief system, it is necessary to get comprehensive support such as perfect data management system, research and development fund investment, balanced human-machine relationship, open digital twin public service platform, etc., so as to fully empower the development of river chief system.