Agricultural land is a complex seminatural and semiartificial ecosystem that is affected by both human activities and natural factors. Clarifying land use and ecological health conflicts in agricultural areas is important for maintaining ecosystem services. Thus, taking the Henan section of the Yellow River (HSYR) as the study area, this study constructed an ecosystem service index (ESI) assessment model to explore the impact of land use change on ecosystem services from 1980 to 2020. Then, the future land use simulation (FLUS) model was used to simulate the effects of different development patterns on ecosystem services heterogeneity in 2035. The results showed that, from 1980 to 2000, the ESI increased from 0.520 to 0.649, but then decreased to 0.509 by the end of 2020 in the HSYR. In any simulation scenarios, urban land expansion continued to encroach on cropland, resulting in the loss of ecosystem services. Especially in the natural development scenario (ND), the ESI may be reduced by up to 2.55%. The results also emphasized that ecosystem services can be protected in the cropland protection scenario (EC). The results of this study enrich the understanding of the impact of human activities on ecological services in agricultural areas and provide new insights into grasping regional food security and ecological stability.