Exploring the spatial and temporal changes of regional aquatic ecosystem services and their relationship with land use is conducive to the protection of regional aquatic ecological environment and the rational development and utilization of land resources, and helps decision makers to improve the regional ecosystem service capabilities and balance the regional ecological functions and agricultural production functions through reasonable land use methods. Longxi River Basin (LRB) in Chongqing, an important ecological barrier in the upper reaches of the Yangtze River, was selected as the research object. The InVEST model was used to study the temporal and spatial variation characteristics of water ecosystem services such as water production, water purification and soil conservation services in the Longxi River Basin in recent 20 years and their effects on different land use types. The results showed that: (1) In the past 20 years, the water ecosystem services of the LRB in Chongqing were generally enhanced and improved, but there were some spatial differences. Although the water yield and water source conservation services of the whole basin had little difference, the forest-intensive area in basin of the water purification services was stronger than that of farm town and industrial agglomeration area. The soil conservation services in basin of water area, construction land and forest land in the central and north-south was stronger than the sloping land on the east and west sides of the basin. (2) Different land use types had different contributions to water ecosystem services. The order of the water yield services from strong to weak as follows: cultivated land > construction land > forest land > grassland > water area. The water conservation capacity from strong to weak as follows: cultivated land > grassland > water area > forest land > construction land. The water purification services from strong to weak as follows: forest land > grassland > construction land > cultivated land > water area. Soil conservation services from strong to weak as follows: water area > construction land > cultivated land > forest land > grassland. (3) In order to balance the supply and regulation services, it was appropriate to take township as a unit to divide the Longxi River Basin into ecological restoration area, agricultural production area and urban development area, and take corresponding ecological measures for each partition.