Urban–rural integration, which aims to balance economic growth with sustainable land use, is becoming an increasingly critical strategy for regional development. This study provides crucial insights into the relationship between land use changes and ecosystem service values (ESVs) in rapidly urbanizing areas by analyzing the urban–rural integration process in Henan Province, a typical agricultural province in China. This research investigated the relationship between land use transformation and ESVs in Henan Province, China, from 1990 to 2020. Utilizing land use data and employing the equivalent factor method and elasticity model, we analyzed shifts in land use and their impacts on ecosystem services across 17 prefecture-level cities. Results indicated a gradual improvement in the urban–rural integration development index of Henan Province, particularly after 2000, but with notable disparities among cities. Zhengzhou, the provincial capital, consistently demonstrated high urban–rural integration development index (URII) values, influencing the integration efforts of neighboring cities. Conversely, peripheral cities exhibited lower integration indices. Notable shifts in land use patterns characterized by diverse transfer dynamics distinctively influenced ESVs across regions. Urban sprawl initially exerted substantial impacts on ecosystem services and stabilized over time. Suburbanization impacts peaked in the early and middle stages, while agricultural intensification initially affected ecosystem services, but their effects diminished with increased efficiency. Ecological restoration efforts consistently enhanced ESVs. The findings contribute to a more comprehensive understanding of the dynamic interactions between land use transitions and ecosystem services in the context of urban–rural integration.