Abstract: As a key parameter of terrestrial ecosystem carbon cycle, the promotion of Net Primary Production (NPP) is of great significance for improving vegetation status, which facilitates ecosystem carbon cycle and regional sustainable development. Taking as the study areas the rocky desertification areas, special ecologically fragile areas in Yunnan, Guangxi and Guizhou, this paper explores the spatial and temporal evolution law, spatial pattern characteristics and driving factors of spatial differentiation of NPP based on the methods of linear regression, spatial autocorrelation and geographical detector. The results show that: ① Preliminary success has been achieved in the control of rocky desertification in the rocky desertification areas of Yunnan, Guangxi and Guizhou, but there remains substantial potential for improvement in vegetation. From 2000 to 2020, the average NPP in the areas increased slowly from 878.99 gC/m²a in 2000 to 908.60 gC/m²a in 2020, with an annual average increase of only 1.486 gC/m²a; ② The spatial pattern of NPP in the rocky desertification areas of Yunnan, Guangxi and Guizhou is relatively stable, but there are some obvious internal differences. In the study areas exist the spatial differentiation characteristics of being higher in southwest, second in south and lowest in north, which corresponds to Yunnan, Guangxi and Guizhou in turn; ③ The spatial distribution of NPP in the study areas shows a significant positive correlation that has a strengthening trend. The local spatial pattern is dominated by high-high (HH) and low-low (LL) concentrations, and NPP has the spatial characteristics that high-value areas tend to be concentrated and low-value areas tend to be adjacent; ④ The spatial-temporal differentiation pattern of NPP in the study areas is a result of the combined effects of natural geographic elements and socio-economic factors, with rainfalls, temperatures, and population densities being the primary influencing factors.