The coupled processes of ecosystem carbon and water cycles are usually evaluated using the water use efficiency (WUE), and improving WUE is crucial for maintaining the sustainability of ecosystems. However, it remains unclear whether the WUE in different ecosystem responds synchronously to the synergistic effect of the same climate factors at daily and monthly scales. Therefore, we employed a machine learning-driven factor analysis method and a geographic detector model, and we quantitatively evaluated the individual effects and the synergistic effect of climate factors on the daily mean water use efficiency (WUED) and monthly mean water use efficiency (WUEM) in different ecosystems in China. Our results showed that (1) among the 10 carbon flux monitoring sites in China, WUED and WUEM exhibited the highest positive correlations with the near-surface air humidity and the highest negative correlation with solar radiation. The correlation between WUEM and climate factors was generally greater than that between WUED and climate factors. (2) There were significant differences in the order of importance and degree of impact of the same climate factors on WUED and WUEM in the different ecosystems. Among the 10 carbon flux monitoring sites in China, the near-surface air humidity imposed the greatest influence on the WUED and WUEM changes, followed by the near-surface water vapor pressure. (3) There were significant differences in the synergistic effects of the same climate factors on WUED and WUEM in the different ecosystems. Among the 10 carbon flux monitoring sites in China, the WUED variability was most sensitive to the synergistic effect of solar radiation and photosynthetically active radiation, while the WUEM variability was most sensitive to the synergistic effect of the near-surface air humidity and soil moisture. The research results indicated that synchronous responses of the WUE in very few ecosystems to the same climate factors and their synergistic effect occurred at daily and monthly scales. This finding enhances the understanding of sustainable water resource use and the impact of climate change on water use efficiency, providing crucial insights for improving climate-adaptive ecosystem management and sustainable water resource utilization across different ecosystems.