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To explore the spatio-temporal evolution patterns and meteorological driving factors of net primary productivity (NPP) in the Kubuqi Desert, MOD17A3HGF NPP data from 2001 to 2023 were used. Methods, including trend analysis, stability analysis, correlation analysis, and importance analysis were applied to examine the spatial and temporal variations in annual average NPP and its relationship with influencing factors such as potential evapotranspiration, precipitation, relative humidity, temperature, vapor pressure deficit, and wind speed. The results showed that the annual average NPP of the Kubuqi Desert from 2001 to 2023 was 108.60 g/(m2·a), ranging from 75.69 g/(m2·a) to 134.97 g/(m2·a), with an overall upward trend showing fluctuations. Spatially, vegetation NPP was primarily distributed in the northwestern part of Huhe Mud Town, the northern part of Jirigalangtu Town, and the northeastern and southern parts of Duguittara Town. The vegetation NPP of the Kubuqi Desert generally exhibited a highly significant increasing trend, with considerable stability fluctuations and significant spatial variability. Future trend analysis suggested that 73.58% of vegetation NPP may exhibit an anti-persistent trend, indicating potential future changes opposite to current trends. The positive correlation between vegetation NPP and temperature and precipitation accounted for 90.56% and 98.07% of total pixels, respectively. The NPP of vegetation had the highest negative correlation with wind speed and relative humidity, reaching 60.57% and 75.57%. Potential evapotranspiration and precipitation were identified as the main factors influencing changes in NPP in the Kubuqi Desert. The research result can provide a scientific basis for the management and sustainable development of desert ecosystems.