SBM-DEA model, network DEA model and bivariate spatial autocorrelation method were used to measure the efficiency of water resources-energy-food nexus system(WEF system)of 30 provincial administrative regions in China from 1997 to 2017, and the spatial-temporal evolution characteristics were analyzed. The results show that during the study period, the efficiency values of water resources, energy and food subsystems in China showed upward trends year by year. The efficiency values of water resources subsystem and food subsystem showed apparent upward trends while the efficiency value of energy subsystem increased slowly. The efficiency value of each subsystem in eastern region was significantly higher than that in central and western regions. There were certain differences in the spatial interaction among the efficiency values of water resources, energy and food subsystems, but the regional distribution range of synergy was relatively consistent. The efficiency values of WEF system in China were on the rise with fluctuation. In terms of regional distribution, the efficiency values were relatively high in eastern and northeastern regions while low in central and western regions. The high efficiency values were mainly distributed in the eastern coastal areas and the middle and lower reaches of the Yellow River Basin, while the western regions were low efficiency areas.