As a typical oasis landscape in the arid region of northwestern China, various ecosystem services (ESs) within the "mountain-oasis-desert" complex system of the Manas River Basin are crucial for regional sustainable development. Based on remote sensing data from 2000 to 2023, this study systematically revealed the spatiotemporal evolution characteristics of ecosystem service value (ESV) in the basin using the equivalent factor method and correlation analysis. The results show: (1) Land use exhibited a pattern of cropland expansion (a net increase of 3,621.11 km2) and grassland reduction (3,493.61 km2 converted out). Cropland expansion dominated in the oasis area, while natural ecological land degradation characterized the mountainous region; (2) The overall ESV of the basin showed a downward trend, with a sharp decline of 33.90% during 2005-2010, resulting in a cumulative reduction of 273.89×108 yuan over 23 years. Among ES types, hydrological regulation service value decreased the most, by 192.53×108 yuan, while the values of food production, raw material supply, and nutrient cycling maintenance services increased. In terms of spatial distribution, high ESV areas were mainly concentrated in the southern mountainous glacial areas and the Manas Lake region, with the desert area being a low-value zone. The ESV of the three geomorphic regions was ranked as: oasis area > mountainous area > desert area. Overall, land use transformation driven by agricultural expansion has exacerbated the degradation of ecological service functions in this region. It is recommended to establish a geomorphic zone-specific regulatory mechanism, focus on coordinating the contradictions between food production and other ecological functions in the oasis area, and promote the orderly management of ecosystem services and the synergetic development of ecology and economy in arid regions.