Net primary productivity (NPP) of vegetation is an important indicator of the carbon cycle of terrestrial ecosystems. Quantitative evaluation of the changing law of NPP is one of the main research contents of carbon cycle mechanism. This article analyzes the spatiotemporal changes of NPP in southwest China from 2001 to 2018 based on land cover and NPP products. We use land transfer matrix and statistical analysis methods to quantitatively describe the amount of NPP change caused by land cover changes and analyze the main reasons for the NPP changes. The results showed that:(1) from 2001 to 2018, the average value of the NPP in the southwest China presented a fluctuating upward trend. (2) The spatial distribution of NPP showed a high in the south and a low in the north. NPP showed a growing trend, mainly in the central and eastern parts of Sichuan, Chongqing, western Guizhou, and eastern Yunnan; NPP indicated a decreasing trend in Yunnan, central and western Sichuan and eastern Guizhou. (3) The conversion of forests, grasslands, and the cultivated land to shrubs and shrubs to forests were land cover types that had a greater impact on the amount of NPP changes. The net increase in NPP caused by land type conversions is 20.643 TgC. (4) The correlation between precipitation and NPP is low. There is some correlation between air temperature and NPP and the vegetation leaf area index has a significant correlation with NPP, indicating that climatic factors have a small impact on NPP, and vegetation growth density has a significant impact on NPP. The implementation of ecological projects such as returning farmland to forest and grassland has led to a decrease in cultivated land and a substantial increase in forest area, which is the leading factor in the NPP increase. This study can provide a reference for the change mechanism of NPP under the background of ecological engineering implementation.