With global warming, the contradiction between the supply and demand of water resources is increasingly prominent in arid areas. Enhancing water resource management is an important way to alleviate the shortage of ecological water supply and improve ecosystem services in arid river basins. However, previous studies have rarely conducted comprehensive function zoning of ecosystem services using two aspects: category (quantity) and strength change (quality), based on the changes in ecosystem services. In this regard, two scientific problems need to be solved:(1) quantifying the temporal and spatial changes of ecosystem services and (2) conducting function zoning of ecosystem services in terms of quantity and quality. To answer these two questions, we took the upper and middle reaches of the Tarim River Basin in China as the study area. According to the eco-environmental characteristics of arid basins, this study measured four key indices: carbon storage (CAS), evapotranspiration (ET), temperature vegetation dryness index (TVDI) and groundwater depth (GWD). We used the related model to quantitatively analyze the spatial and temporal distribution of these four indicators and the spatial aggregation characteristics of increases and decreases. We used the Reclassify tool of ArcGIS 10.5 to classify areas with more than two important zones as high-quantity ecosystem services zones. We used factor analysis, combined with Quantile, to divide ecosystem service quality into high-quality and low-quality zones. Considering the quantity and quality of ecosystem services, we divided ecosystem services into important, general, sensitive and fragile ecosystem services zones. Based on comprehensive zoning results during 2000–2018, an ecosystem services restoration zoning was determined. We used correlation analysis to analyze the basic drivers of changes in these four indicators. The results showed that during 2000–2018, CAS and ET in the Tarim River Basin increased by 0.2% and 15.3%, respectively, TVDI decreased by 22.5% and GWD rose by 1.7%. In 2018, the hot spots of CAS, ET, TVDI and GWD accounted for a small proportion of the whole study area, accounting for 3.8%, 5.9%, 9.0% and 1.4%, respectively. Compared with 2000, the high-quantity zone of ecosystem services increased by 10.7% and the high-quality zone of ecosystem services increased by 2.0% in 2018. This clearly showed that water diversion and riverway loss were the main factor driving changes in ecosystem services. In terms of maintaining groundwater depth and increasing vegetation coverage, specific counter measures and suggestions for increasing the number of ecosystem services (“increment”) and improving the quality of ecosystem services (“quality improvement”) were proposed. This study can provide a scientific reference for achieving optimal management of water resource systems for similar river basins in arid regions.