Ecosystem services (ESs) are crucial for sustainable development, as they impact human well-being. However, changes in land use/land cover (LULC) caused by climate change and social development can negatively affect ESs, particularly in arid river basins. This study focuses on current and future changes in LULC in the Kaxghar River Basin (KRB) in Xinjiang, China, to determine how these changes will affect the region’s ESs. The integrated PLUS-InVEST model was used to investigate the spatiotemporal distribution and changing patterns of habitat quality (HQ) and carbon storage (CS) under the natural increase scenario (NIS), economic development scenario (EDS), and water protection scenario (WPS). Additionally, the Ecosystem Service Contribution Index (ESCI) was also calculated to evaluate the contribution of LULC changes to ESs. The results show the following: (1) from 2000 to 2020, the average value of HQ in the KRB gradually decreased from 0.54 to 0.49 and CS trended slightly upward, with a total increase of 0.07 × 106 t. Furthermore, the changes in CS were highly consistent with changes in LULC. (2) From 2020 to 2030, the area of low-grade (0–0.2) HQ saw a continuous increase, with the fastest growth occurring in 2030 under the EDS. Meanwhile, under the WPS, HQ significantly improved, expanding by 1238 km2 in area. Total CS under the three test scenarios tended to decline, with the NIS showing the smallest decrease. (3) The expansion of cropland and unused land had a negative impact on ESs, particularly on CS, whereas the conversion to grassland and forestland had a significant positive impact. In conclusion, these insights will enrich our understanding of ESs in the study area and contribute to balancing the relationship between ecological conservation and socioeconomic development in the Kaxghar River Basin, as well as in other parts of China’s arid Northwest and similar regions around the world.