The contradiction between the territorial governance model and the mobility of water pollution makes results in inefficiency of water pollution governance. This paper establishes a reasonable framework for collaborative governance of water pollution in China’s river basin, then measure the degree of synergy and analyze its influencing factors. Based on the provincial and municipal data from 2010 to 2018, this paper employs the Euclidean Distance, generalized linear efficacy coefficient method and panel data measurement model to evaluate. The Research Findings are as follows: Firstly, according to the situation of water pollution in China, seven coordination zones should be established. Secondly, the synergy degree shows a divergent trend since the promotion of chief system in China. Thirdly, Intergovernmental cooperation and R&D investment will deepen the collaborative governance of water pollution. Fourthly, differences in the level of regional economic development and industrial structure will hinder the collaborative governance of water pollution. Fifthly, the establishment of environmental protection organizations, differences in FDI, and differences in human capital have no significant impact on collaborative governance. This paper providing inspiration for coordination mechanism in ecological civilization and promoting the implementation of 14th Five-Year Plan.