Southwestern China is an important ecological barrier and the major area supplying water to our country and most of East Asia. In light of the impacts of global change, rapid economic development, excessive resource utilization, and a series of ecological construction projects, land cover of southwestern China has changed significantly over the last 20 years. This has had great consequences for the eco-environment. After assessing land cover datasets of China in 1990, 2000, and 2010, we propose a land cover classification system that is appropriate for southwestern China. We analyze the spatial-temporal patterns, changing characteristics, and potential causes. In addition, we estimate fractional vegetation cover from 2000 to 2010 using the dimidiate pixel model, based on MODIS-NDVI data. Results show that:1) in 2010, forest was the dominant land cover type, occupying 29.08%, followed by grassland, which covered 24.11%. 2) From 1990 to 2010, areas of forest, wetland, and artificial surface increased by 1.39%, 5.86% and 48.57%, respectively, but areas of shrubland, arable land, and barren land decreased by 2.21%, 2.88% and 0.64%, respectively. The conversion areas are mainly distributed in the regions where the ecological restoration programs are carried out, the urban circle, the earthquake stricken area, the Three Gorges Reservoir Region, the Three-River Headwater on Qinghai-Tibet Plateau, and the southern Yunan province. 3) The changes in fractional vegetation cover of forest, shrub and grassland showed an overall upward trend in 2000s, but forest and shrub showed a trend of degradation in the Wenchuan earthquake-stricken area, Hengduan Mountains, and southern Yunnan province; grassland also deteriorated in the southeastern Tibet Plateau and western Sichuan Plateau. In summary, in the last two decades, although climate change has affected land cover, policy regulation and economic driving forces are still the primary causes of land cover changes across southwestern China.