It is significant to study the impact of land-use changes on vegetation net primary productivity (NPP) both for elucidating the relationship between the carbon assimilation ability of vegetation and the land-use changes on a regional scale, and for maintaining stability in ecosystem structures. By using the section of the Three Gorges Reservoir Area (TGRA) in Chongqing as a study area, we analyzed the spatio-temporal distribution of NPP and the impact of land-use changes on the regional NPP in term of landscape ecology based on the land-use maps and remote sensing data MOD17A3 from 2000 to 2015. The results revealed that the average annual NPP did not change much in over 16 years and it spatially decreased from east to west. During the study period, the areas of woodland increased, whereas the areas of farmland and grassland declined. The total NPP increased from 25.6 TgC to 28.5 TgC, in which comprised 44% in farmland, 40% in woodland, and 14% in grassland. The rates of NPP variations induced by land-use changes in 2000-2005, 2005-2010, and 2010-2015 were 26.49%, 59.76%, and 17.27% respectively. Shannon's diversity index (SHDI) and patch density (PD) were positively correlated with NPP, whereas the aggregation index (AI) was negatively correlated with NPP. Both the types and their changes of landscape patterns increased NPP. To improve the regional vegetation NPP, some measures, which includes optimizing the land-use pattern, increasing the landscape heterogeneity and patch density, emphasizing the cultivation of young forest, and controlling the number of mature forests, need to be adopted by local governments in the future.