In this study, we developed an evaluation index system for green total-factor water-use efficiency (GTFWUE) which reflected both economic and green efficiencies of water resource utilization. Then we measured the GTFWUE of 30 provinces/municipalities/autonomous regions (hereafter provinces) in China (not including Tibet, Hong Kong, Macao, Taiwan as no data) from 2000 to 2018 using a minimum distance to the strong frontier model that contained an undesirable output. We further analyzed the regional differences and spatial correlations of GTFWUE using these values based on Global and Local Moran’s I statistics, and empirically determined the factors affecting GTFWUE using a spatial econometric model. The evaluation results revealed that the GTFWUE differed substantially between the regions. The provinces with high and low GTFWUE values were located in the coastal and inland areas of China, respectively. The eastern region had a significantly higher GTFWUE than the central and western regions. The GTFWUEs for all three regions (eastern, central, and western regions) decreased slowly from 2000 to 2011 (except 2005), remained stable from 2012 to 2016, and rapidly increased in 2017 before decreasing again in 2018. We found significant spatial correlations between the provincial GTFWUEs. The GTFWUE for most provinces belonged to the high-high or low-low cluster region, revealing a significant spatial clustering effect of provincial GTFWUEs. We also found that China’s GTFWUE was highly promoted by economic growth, population size, opening-up level, and urbanization level, and was evidently hindered by water endowment, technological progress, and government influence. However, the water-use structure had little impact on GTFWUE. This study fully demonstrated that the water use mode would be improved, and water resources needed to be used more efficiently and green in China. Moreover, based on the findings of this study, several policy recommendations were proposed from the aspects of cross-regional cooperation, economy, society, and institution.