Sichuan-Chongqing region is located in the southwest of China and the upper reaches of the Yangtze River. The terrain conditions are complex, and the eco-environment in the region is relatively sensitive to climate change. As China's modern agricultural development zone and importantly ecological barriers in the middle and upper reaches of the Yangtze River, the research about the relationship between regional vegetation coverage and climate change is of great significance to the ecological civilization construction and agricultural sustainable development of the region. Based on the normalized difference vegetation index (NDVI), and meteorological data (temperature and precipitation), we analyzed the characteristics of the spatio-temporal changes of vegetation cover and its response to climate factors in the Sichuan-Chongqing region from 1999 to 2018 from the perspective of agricultural geomorphology by using Sen trend analysis, Manna-Kendall test and partial correlation analysis. The results indicated that:(1) the NDVI in the Sichuan-Chongqing region and each agricultural geomorphic area exhibited a significant upward trend in the past 20 years, and the growth rate was as follows:Mountain area in Sichuan Basin (0.0073/a) > Sichuan Basin (0.0063/a) > Highland of Southwestern Sichuan (0.0050/a) > Western Sichuan Alpine and Plateau (0.0026/a). The overall inter-annual change rate was 0.0047/a. (2) About 91.51% of the NDVI pixel values in the Sichuan-Chongqing region were positive, showing a general distribution pattern of high in the east and low in the west. The highest value of NDVI was 0.60 in the Mountain area in Sichuan Basin, and the lowest value of NDVI was 0.44 in the Western Sichuan Alpine and Plateau. (3) The NDVI was positively correlated with temperature and precipitation in the Sichuan-Chongqing region, and the correlation between NDVI and temperature (r=0.707, P<0.01) was stronger than that of precipitation (r=0.535, P<0.05). In terms of space, the area with significantly positive correlation between NDVI and temperature and precipitation accounted for 39.31% and 18.92%. (4) In different agricultural geomorphic regions, climate change had obviously different effects on vegetation growth. In the Western Sichuan Alpine and Plateau, the NDVI was positively correlated with temperature, but not with precipitation. The NDVI was significantly affected by temperature and mainly distributed in the Aba-Zoige-Hongyuan flat plateau and Shiqu hilly plateau areas. In the Sichuan Basin and Mountain area of Sichuan Basin, the NDVI was positively correlated with temperature and precipitation, especially parallel ridge valley and low hilly area in the northeast, which was significantly affected by temperature and precipitation. The results help to further understand the relationship between vegetation and climate change in the Sichuan-Chongqing region, and provide scientific support for promoting ecological construction and development of the region.