This study aims to improve the level of water ecological civilization (WEC) in the urbanization process based on the data of prefecture-level cities in Jiangxi, China, from 2011 to 2020. This paper applies spatial analysis methods such as the natural fracture method, barycenter transfer model, and standard deviation ellipse method to explore the spatiotemporal evolution characteristics of WEC and the impact of new urbanization (NU) on WEC. The NU pilot construction is further regarded as an exogenous impact, and the “net effect” of the NU pilot policy on WEC is tested. The results showed that (1) the spatial distribution pattern of the east–west polarization of WEC was broken, and a spatial distribution pattern of strong in the north and weak in the south was gradually formed. (2) NU contributes to improving the WEC level, among which population, digital, and green urbanization can significantly promote the WEC level, while economic urbanization impedes the improvement of the WEC. This conclusion is still valid following a series of robustness tests. (3) heterogeneity analysis showed that the impact of NU in improving the level of WEC is more evident in cities with scarce water resources, non-resource-based cities, and non-old industrial base cities after the implementation of NU planning. (4) NU’s pilot policy can help improve the WEC level in the region and the WEC level in neighboring regions through the spillover effect of policy. Therefore, it is necessary to make use of the superimposed effect of multidimensional urbanization based on urban characteristics, implement differentiated policy, break administrative barriers, make use of the spatial spillover effect of pilot policy, and improve the WEC level.