Water use efficiency (WUE), the ratio of gross primary productivity (GPP) over evapotranspiration (ET), is a critical ecosystem function. However, it is difficult to distinguish the individual effects of climatic variables and leaf area index (LAI) on WUE, mainly due to the high collinearity among these factors. Here we proposed a partial least squares regression‐based sensitivity algorithm to confront the issue, which was first verified at seven ChinaFlux sites and then applied across China. The results showed that across all biomes in China, monthly GPP (0.42–0.65), ET (0.33–0.56), and WUE (0.01–0.31) showed positive sensitivities to air temperature, particularly in croplands in northeast China and forests in southwest China. Radiation exerted stronger effects on ET (0.55–0.78) than GPP (0.19–0.65), resulting in negative responses (−0.44 to 0.04) of WUE to increased radiation among most biomes. Increasing precipitation stimulated both GPP (0.06–0.17) and ET (0.05–0.12) at the biome level, but spatially negative effects of excessive precipitation were also found in some grasslands. Both monthly GPP (−0.01 to 0.29) and ET (0.02–0.12) showed weak or moderate responses to vapor pressure deficit among biomes, resulting in weak response of monthly WUE to vapor pressure deficit (−0.04 to 0.08). LAI showed positive effects on GPP (0.18–0.60), ET (0–0.23), and WUE (0.13–0.42) across biomes, particularly on WUE in grasslands (0.42 ± 0.30). Our results highlighted the importance of LAI in influencing WUE against climatic variables. Furthermore, the sensitivity algorithm can be used to inform the design of manipulative experiments and compare with factorial simulations for discerning effects of various variables on ecosystem functions.