The ecosystem of extra-high mountain areas is very fragile. Understanding local vegetation changes is crucial for projecting ecosystem dynamics. In this paper, we make a case for Himalayan mountain areas to explore vegetation dynamics and their influencing factors. Firstly, the interannual trends of the normalized difference vegetation index (NDVI) were extracted by the Ensemble Empirical Mode Decomposition (EEMD) algorithm and linear regression method. Moreover, the influence of environmental factors on interannual NDVI trends was assessed using the Random Forests algorithm and partial dependence plots. Subsequently, the time-lag effects of seasonal NDVI on different climatic factors were discussed and the effects of these factors on seasonal NDVI changes were determined by partial correlation analysis. The results show that (1) an overall weak upward trend was observed in NDVI variations from 1982 to 2015, and 1989 is considered to be the breakpoint of the NDVI time series; (2) interannual temperature trends and the shortest distance to large lakes were the most important factors in explaining interannual NDVI trends. Temperature trends were positively correlated with NDVI trends. The relationship between the shortest distance to large lakes and the NDVI trend is an inverted U-shaped; (3) the time-lags of NDVI responses to four climatic factors were shorter in Autumn than that in Summer. The NDVI responds quickly to precipitation and downward long-wave radiation; (4) downward long-wave radiation was the main climate factor that influenced NDVI changes in Autumn and the growing season because of the warming effect at night. This study is important to improve the understanding of vegetation changes in mountainous regions.