Water use efficiency(WUE) is an important indicator to measure utilization ratio of water resources, which has obvious response to climate change. Ecological water shortage is serious in karst area of Southwest China, and water resource utilization problem needs to be solved urgently. However, the response of water use efficiency to meteorological factors is still unclear. In this paper, MODIS gross primary productivity (GPP) and evapotranspiration (ET) data sets were used to calculate water use efficiency in karst area of Southwest China. Combined with meteorological and normalized difference vegetation index (NDVI) data, the temporal and spatial variation characteristics of water use efficiency and its response to meteorological factors were revealed by using the Theil-Sen Median trend analysis and Pearson correlation analysis. The results showed that the change trend of the annual water use efficiency was similar with the active growing season water use efficiency (AGS-WUE) in the karst area of Southwest China from 2000 to 2014. In spring and autumn, water use efficiency demonstrated an upward trend and a downward trend in summer. The annual water use efficiency showed an upward trend, which was negatively correlated with precipitation, positively correlated with temperature in karst areas, while negatively correlated with temperature in non-karst areas. The growth of NDVI was the main driving factor. Annual water use efficiency and AGS-WUE increased gradually from southeast to northwest. The water use efficiency in non karst areas was higher than that in most karst areas. In general, water use efficiency in high altitude areas was higher than that in low altitude areas. Temperature, altitude and the degree of karst development affected water use efficiency in karst areas comprehensively. The results of this study can provide theoretical reference for improving the water use efficiency of karst ecosystem.