The Aral Sea started shrinking since the 1960s due to natural factors and human activities; however, the relationship between land cover change and ecosystem services (ES) in the Aral Sea basin has not been fully studied. To analyze and explore the spatiotemporal variation characteristics of ecosystem service values (ESVs) in this region, we used the European Space Agency CCI Global Land Cover product with a spatiotemporal resolution of 300 × 300 m and the annual scale. The land use data of 1993, 1998, 2003, 2008, 2013, and 2018 in the study area were extracted, the study area’s ESV in the corresponding years was calculated, and the temporal and spatial evolution characteristics were analyzed. Additionally, the change rate and sensitivity were analyzed. The results revealed that the area of urban land, bare land, grassland, wetland, and cropland in the Aral Sea basin increased from 1993 to 2018; water body and forestland decreased. The integrated value of water bodies, cropland, and grassland ES accounted for more than 96% of the total ESV; the change rate of land use types differed. Urban land and water changed the fastest; cultivated land, woodland, grassland, and wetland changed the slowest. From 1993 to 2018, the total ESV of the Aral Sea basin decreased from 455.10 to 414.56 billion (Overall decrease = − 8.91%). The ESV study shows that the water area decreased sharply from 1993 to 2018, resulting in a loss of USD 46.84 billion. Biodiversity, food production, and water regulation were the main ES, accounting for 78.5% of the total ESV. The ESV of the Aral Sea basin declined from 1993 to 2018, and significant differences were observed among its regions. Some regions should thus focus on this aspect. A close correlation was observed between the ESV and land use. Hence, effective land use policies can control the expansion of cropland; protect water bodies, ecological environments, grassland, and forestland; and promote a more sustainable ecosystem.