Abstract: Under global warming, there remains considerable uncertainty regarding the impacts of meteorological and soil drought on vegetation. Exploring the synergistic impacts of soil moisture (SM) and meteorological drought holds significant importance for assessing drought risk and ecosystem health. Therefore, based on the standardized precipitation evapotranspiration index (SPEI) and leaf area index (LAI), this study analyzed the LAI, meteorological drought, and SM in Yunnan Province from 2001 to 2020. Then, it further investigated the contributions of SM at different depths and SPEI at varying temporal scales to LAI using interpretable machine learning methods, specifically SHapley Additive exPlanations (SHAP). The results indicate that from 2001 to 2020, the LAI in Yunnan exhibited a fluctuating upward trend with an overall growth rate of 0.37 m² per decade. The SM at varying depths showed a weak decreasing trend, with the most pronounced decrease observed in SM_Layer4. The SPEI values predominantly ranged from -1.1 to -1.0 across the four time scales, with an average drought duration below 3.5 months in most areas. Moreover, both LAI and SM decreased with the intensification of meteorological drought, with the most pronounced reduction in SM occurring in shallow layers. Notably, severe and extreme meteorological droughts exerted stronger influences on LAI, while moderate and lower drought levels had impacts on LAI with minimal differentiation. Compared to SM, the SPEI across the four time scales had subordinate impacts on LAI. Specifically, in humid areas, deep SM exhibited a contribution to LAI reaching up to 74.3%~77.7%, while in semi-humid and semi-arid areas, shallow SM contributed more to LAI than deep SM. The results of this study provide a scientific reference for planning sustainable development pathways of ecosystems in Yunnan Province.