The spatio-temporal patterns of vegetation coverage in Yunnan Province from 2000 to 2016 were analyzed using moderate resolution imaging spectrometer (MODIS) normalized difference vegetation index (NDVI) data. Maximum value composites, linear regression methods, and partial correlation analyses were used to investigate the monthly and annual NDVI variations, analyze the spatial distribution and changes in the NDVI, and examine the relationships between the NDVI and climatic factors. The results showed that the average NDVI value for Yunnan Province was 0.55 from 2000 to 2016. The higher NDVI values (>0.8) were mainly distributed in the southern part of Yunnan Province. In contrast, the northwest part and central urban region had lower NDVI. Annual NDVI increased significantly from 2000 to 2016 (P < 0.05), and the slope of the trend line was 0.0036. The seasonal NDVI and the growing season NDVI also showed increases. Autumn had the fastest NDVI growth rate (0.0063), followed by spring (0.0044), winter (0.0042), and summer (0.0010). The increasing rate of NDVI in the growing season (0.0025) was higher than that in summer. The vegetation improvement area was significantly greater than the degradation area, and the area of increasing trend accounted for 79.80% of the total vegetation coverage. The area of increased vegetation coverage was mainly concentrated in the northeast and east regions, and the decreased vegetation area was mainly concentrated in northwest and central regions. Precipitation had a crucial effect on the NDVI variation in spring, summer, and autumn, but temperature was the main controlling factor in winter. There was a clear difference in the relationships between NDVI and temperature and precipitation among different months of the growing season, and there was a time lag in the response of NDVI to precipitation.