This study aims to examine the individual and combined effects of soil moisture (SM) and vapor pressure deficit (VPD) on ecosystem productivity in Southwest China. Utilizing the community land model (CLM) to simulate the regional soil moisture and vapor pressure deficit, we analyzed their impacts on ecosystem productivity through a data binning approach and employed sun-induced chlorophyll fluorescence yield (SIFyield) as a productivity indicator. Our findings highlight a significant coupling effect between SM and VPD, which diminishes with finer temporal data resolution. The data binning analysis indicates that VPD has a predominant influence on SIFyield across 70% of the study area, whereas SM is more influential in the remaining 30%. Notably, the correlation between SIFyield and SM, modulated by VPD, is stronger in forest and shrubland ecosystems, whereas in grasslands, the influence pattern is reversed, with VPD having a more significant impact. The study concludes that in Southwest China, ecosystem productivity is more significantly affected by VPD than by SM.