The various production factors of the autonomous region are concentrated in the Ningxia Yellow River Economic Zone. Ecosystem service value of it is more and more significant than ever. Taking the Ningxia Yellow River Economic Zone for example, based on the platform of ArcGIS, this paper adopts the equivalent factor method to estimate the value of 11 ecological service functions for 6 major ecosystems, and clarifies the internal structure, temporal and spatial distribution characteristics and trends of ecosystem service value, then puts forward ecological protection countermeasures to serve the ecological protection and high–quality development of the leading areas in Ningxia section of the Yellow River Basin. The results show that the ecosystem service value is high in the middle and low in the margin of the economic zone, high in the basins and mountains, low in the deserts and hilly area. The amount order of ecosystem services the value is regulation service value > supply service value > support service value > aesthetic value; ecosystem services are mainly dominated by hydrological regulation, climate regulation, water supply and air regulation services, accounting for 59.07%, 8.97%, 5.02% and 4.91%, respectively. In general, ecological services value shows an increasing trend, but compared with the speed of economic development, it is still in a state of low coordination. In the next step, under the premise of protecting ecological functions by taking into account the aesthetic value, the clean energy such as solar and wind energy in the desert and hilly areas should be strengthened to enhance the ecological value for the low ecosystem service value region and fragile ecological areas.