The Conversion of Cropland to Forest Project (CCFP) can improve the ecological benefits, but also threaten food security. It is important to create a win-win situation in economic development and environmental protection. In the context of returning farmland into forest, in order to further promote ecological protection and sustainable development, it is essential to identify the trade-offs and synergies of multiple ecosystem services at different spatial scales. Under the influence of human activities and the natural environment, the relationship of ecosystem services changes over time and spatial scales. Studying the spatio-temporal dynamics of these relationships is of great significance for understanding the trends in ecosystem services, evaluating the effects of returning farmland into forest, and determining appropriate land use patterns and ecological restoration measures. However, it is still a challenge to fully understand the temporal and spatial dynamics of ecosystem service relationships in the Loess hilly and gully region before and after the CCFP, due to the research on different types of ecosystem services, as well as the information about the adaptable units of ecosystem service management is often insufficient. Therefore, the purpose of this study is to identify the relationship among ecosystem services at the municipal and county levels before and after the CCFP. Using physical methods, five key ecosystem services in Yan'an City, including crop production, carbon storage and sequestration, habitat quality, soil conservation, and water yield were quantitatively evaluated from 1988 to 2018 by InVEST model. The tradeoffs and synergies among five key ecosystem services, and their temporal and spatial variation characteristics, were analyzed through partial correlation analysis. The results showed that:(1) Affected by land use changes, the interannual trends of crop production and soil conservation in Yan'an fluctuated greatly; the crop production level showed a fluctuating upward trend; the soil conservation decreased before the CCFP, fluctuated and increased after the CCFP; the carbon storage and sequestration and habitat quality showed a gradually increasing trend; the water yield decreased gradually. (2) Ecosystem services were closely related to land use patterns. Areas with high carbon storage and sequestration, habitat quality, and areas with low water yield, varied with changes in woodland distribution patterns. (3) Within the research period in Yan'an city, the ecosystem services were dominated by synergistic relationships, which mainly occurred between carbon storage and sequestration, habitat quality, soil conservation, and crop production. While water yield with other ecosystem services showed a trade-off relationship. (4) The differences in ecosystem services between city and county mainly occurred in habitat quality and soil conservation.