Based on MODIS-EVI and meteorological data, methods of Maximum Value Composite (MVC), dimidiate pixel model, trend analysis, and correlation analysis were used to investigate the temporal and spatial changes of Fractional Vegetation Coverage (FVC) and to clarify driving factors on dynamic changes of enhanced vegetation index (EVI) from 2001 to 2015 in Southwest China. Our results showed that: (1) from 2001 to 2015, the EVI in Southwest China showed a volatility increasing trend with the change rate of 0.1%/a. However, the spatial heterogeneity of EVI dynamic was significant, showing a trend of gradually decreasing from southeast to northwest of the study area. (2) Southwest China was dominated by the high and extremely high FVC types, while the areas of extremely low FVC only accounted for about 8.6% of the study area. The areas with increased FVC were concentrated in Beihai-Qinzhou of Guangxi Autonomous Region, Shaotong-Bijie-Zunyi of Guizhou Province, Guangyuan-Guang'an of Sichuan Province and Naqu of Tibet Autonomous Region. The areas with decreased FVC were mainly located in the Lhasa-Ali of Tibet Autonomous Region and Chengdu-Aba-Garzê of Sichuan Province. (3) The changes of the EVI had positive correlations with temperature and precipitation from 2001 to 2015. At a significant level of 0.05, the areas with EVI changes mainly driven by precipitation accounted for about 3.4% of the study area, which were distributed in patches at the junction of Qinghai Province and Tibet Autonomous region, as well as some parts of Yunnan and Guangxi Province. The areas with EVI changes mainly driven by temperature accounted for about 1.6% of the study area, which were distributed sporadically throughout Southwest China. Moreover, the areas with EVI changes mainly driven by both temperature and precipitation accounted for approximately 7.2% of the study area, which were distributed in the northern Ali area of Tibet Autonomous region, the Sanjiangyuan headwater area of Qinghai Province, and the junction of Sichuan and Guizhou Provinces. Therefore, the EVI dynamics were mainly driven by non-climate factors in most areas of Southwest China.