Based on net primary productivity (NPP), the evaluation of the importance of biodiversity maintenance functions in arid watershed can provide a scientific basis for ecological security construction. Based on the MODIS13Q1 data and environmental data of the Manas River Basin, this study used the CASA model to estimate the vegetation NPP in the Basin from 2001 to 2020, and combined terrain factors to construct an evaluation model for the importance of biodiversity maintenance functions in the Basin. Effects of factors such as soil type on the spatial heterogeneity of the NPP in the watershed were analyzed by GeoDetector. The results show that:(1) in the past 20 years, the average NPP of vegetation in the basin has shown an upward trend, with the high values were concentrated in the low hilly belt of mountainous area and the central of oasis area, and the low-value areas were distributed in the desert ecological area; (2) From the average NPP value of different land use types in the Basin, the order was the cultivated land>forest land>grass land>construction land>unused land>water area; (3) The numerical ranges of the general important area, medium important area, important area and extremely important area of the biodiversity maintenance function of the basin are:0-0.12, 0.12-0.22, 0.22-0.47 and 0.47-0.84, accounting for 20.17%, 20.14%, 19.91% and 19.85% of the total area of the Basin. The central part of the oasis area and the low mountain and hilly belt of the mountain area are extremely important areas for the maintenance of biodiversity in the Basin; (4) The annual average precipitation and soil type are the factors with the strongest explanatory power of spatial differentiation of NPP in the Basin. The effects of natural factors on NPP in the Basin showed nonlinear enhancement and two-factor enhancement, with the interaction between annual average precipitation and altitude being the strongest (q=0.44), followed by the interaction with the annual average total solar radiation (q=0.42).