Soil temperature and moisture are the key variables that control the overall effect of climate and topography on soil and vegetation in alpine regions. However, there has been little investigation of the potential soil temperature and moisture feedbacks on climate changes in different alpine ecosystems and their impact on vegetation change. Soil temperature and moisture at five depths were measured continuously at 10-min intervals in three typical ecosystems (Kobresia meadow (KMd), Achnatherum splendens steppe (ASSt), and Potentilla fruticosa shrub (PFSh)) of the Qinghai Lake watershed on the northeast Qinghai-Tibet Plateau, China. The findings of this study revealed that the KMd and PFSh sites had relatively low soil temperature and high soil moisture, whereas the ASSt site had relatively warm soil temperature and low soil moisture. The soil and vegetation characteristics had important effects on the infiltration process and soil moisture regime; about 47%, 87%, and 34% of the rainfall (minus interception) permeated to the soil in the KMd, PFSh, and ASSt sites, respectively. In the context of the warming climate, changes to soil moisture and temperature are likely to be the key reasons of the alpine meadow deterioration and the alpine shrub expansion in the alpine regions.