The water environment quality is not high, the spatial and temporal distribution of water resources is uneven, and the water quality-induced water is in shortage in the world. Strengthening the construction of water ecological civilization is one of the important measures to solve these problems. We took China’s Jiangxi Province and its prefecture-level cities as the research object, the water ecological civilization level was measured from the two dimensions of time and space by principal component analysis, and based on the panel data of prefecture-level cities from 2011 to 2020, the panel data model was used to empirically analyze the impact factors of water ecological civilization. The results show that: (1) The level of water ecological civilization in Jiangxi Province shows a fluctuating upward trend, in which the level of water ecological civilization first increased, then decreased, and then increased from 2013 to 2020. (2) Water ecology is the key to affecting water ecological civilization, and cities with abundant natural endowments of water resources have higher scores for water ecological civilization. (3) There are significant differences in the level of water ecological civilization in different cities in Jiangxi Province; the level of water ecological civilization in southern Jiangxi and central Jiangxi is generally higher than that in northern Jiangxi; among the 11 prefecture level cities, Ji’an, Fuzhou, Jiujiang, Yichun, Ganzhou, and Shangrao have a high level of water ecological civilization. (4) Industrial structure, educational investment, and government governance level have significantly improved the level of water ecological civilization. Environmental pollution is not conducive to improving the level of water ecological civilization. There is an inverted U curve between the level of urbanization and the level of water ecological civilization. Accordingly, all prefecture-level cities in Jiangxi Province need to implement new development concepts and innovation-driven strategy, make up for shortcomings, and strengthen weak points according to their own natural endowments of water resources, such as optimizing the industrial structure, increasing investment in education, improving the level of government governance, and strengthening the connotation construction of urbanization, so as to promote the construction of water ecological civilization in Jiangxi Province. The research results also provide a reference for other countries similar to Jiangxi Province to solve the problem of water pollution, alleviate the pollution-induced water shortage, and improve the water ecological environment in the process of economic development.