Comprehending the spatio-temporal dynamics of ecological service functionalities and appropriately categorizing clusters of ecosystem services are vital for ecosystem management and policy formulation. The objective of this research is to disclose the spatio-temporal evolution and interrelations of biodiversity conservation, water production, carbon storage, soil preservation, net primary production of vegetation, and crop yield in the Yangtze River Delta urban group from 2000 to 2020. It employs spatially constrained (SC) K-means clustering to distinguish ecosystem service clusters and designates management zones for ecosystem service functions. The findings indicate that: (1) There's a spatial pattern of "high in the southwestern mountains, low in the northeastern plains" for biodiversity conservation, water yield, carbon storage, soil protection, and net primary production of vegetation, while the food production trend is contrary; (2) The spatial differences in the six types of ecosystem services demonstrate notable human activity and natural climate influences, with a trade-off observed between food production and other ecosystem services; (3) Utilizing the SC K-means identified ecosystem service clusters, the area is divided into six ecological functional zones: the primary grain production zone, dense human activity zone, Anhui-Zhejiang ecological conservation zone, Dabie Mountain ecological reserve, Wanjiang ecological transition belt, and Yangtze River Delta core conservation area, offering tailored ecological management recommendations for each zone. The research offers a theoretical foundation and practical insights for guiding the zoning in territorial spatial planning.