The Henan Yellow River Basin is an ecological support belt for the entire basin. It holds a significant position in high-quality development and ecological conservation within the Yellow River Basin. However, due to improper development activities, such as urban expansion and deforestation of farmland, certain areas of the region have encountered a series of ecological issues, posing significant challenges to ecosystem services. The scientific foundation for the sustainable development of the ecological environment in the Henan Yellow River Basin is established by research on the evolution characteristics and driving factors of ecosystem service functions. This study focuses on the Henan Yellow River Basin, by introducing remote sensing data and biomass data, assessing the spatiotemporal variations in ecosystem service by the InVEST model—including carbon stock, water yield, and soil conservation—from 2000 to 2020. It analyzes the ecosystem service functions of different land use types. It employs the Geodetector to identify the dominant driving factors behind the changes in these functions based on the improved InVEST model evaluated results. The findings reveal that from 2000 to 2020, total carbon stock increased by 1.86%, carbon stock per unit area rose by 1.81%, and the spatial distribution remained largely stable. The high-value regions were clustered in the west and part of the north, primarily consisting of forest land. Carbon stock capacity in other regions, mainly farmland and construction land, was poor, with forest land having the strongest carbon sequestration capacity, followed by grassland. Total water yield decreased by 20.08%, and water yield per unit area decreased by 20.03%, with a spatial distribution closely following the trend of precipitation distribution. The high-value regions were clustered in the south, primarily in forest land and farmland. The total amount of soil conservation decreased by 19.96%, and soil conservation per unit area decreased by 19.93%, with spatial distribution patterns similar to those of carbon stock and water yield. The high-value regions were concentrated in the southwestern and northern forested regions, while soil conservation capacity in areas primarily consisting of farmland and construction land was weaker. The divergence of carbon stock was most influenced by population density, water yield by precipitation, and soil conservation by slope. In conclusion, during the study period, while carbon storage increased, the significant decline in water yield and soil conservation highlighted critical issues in the ecosystem service functions of the region. These findings indicate the need for targeted conservation measures and sustainable development strategies to address the decline in ecosystem services and mitigate adverse environmental impacts, ensuring the long-term health of the region’s ecosystems. This study offers an in-depth understanding of the differentiation of ecosystem service functions and their driving factors, enabling precise assessment of regional ecosystem services, and providing a theoretical foundation for formulating effective regional ecological conservation policies.