The identification of ecosystem service bundles is the key to the management and optimization of regional ecosystem services. This study quantified seven ecosystem services including water yield (WY), water conservation (WC), soil conservation (SC), habitat quality (HQ), water purification (WP), net primary productivity (NPP) and carbon storage (CS) in the Huaihe River Basin in 2000, 2010 and 2020. Based on Self-Organizing Feature Map, ecosystem service bundles are identified, and the spatio-temporal variations of ecosystem service bundles are discussed. The results show that: The land use type is primary cultivated land, accounting for 67.83% of the basin area in 2020, followed by build-up land area. From 2000 to 2020, the area of cultivated land, forest land and grassland all show a decreasing trend. The primary pattern of land use change is that the expansion of build-up land leads to the reduction of cultivated land area. From 2000 to 2020, WP, NPP and WC show an upward trend, and WC has the largest increase. CS and HQ showed a decreasing trend. The ecosystem services are spatiotemporal heterogeneity, and the high-value ecosystem services are mostly located in the mountainous areas of the southwest and the hilly areas of the northeast. The high value area of WY is widely distributed and affected by the spatial distribution pattern of rainfall. The high value area of NPP is mainly distributed in the southern mountainous area and the eastern coastal area, while the low value area is mainly distributed in the northwestern part of the basin and the northern hilly plain area of the southern mountainous area. The high value of SC is divided in the southern mountainous area and the northern hilly plain area of the southern mountainous area. Five ecosystem service bundles were identified: Key ecological bundle, WP bundle, WY bundle, NPP bundle and Ecological transition bundle. The area of Key ecological bundle and Ecological transition bundle has increased, and the ecosystem services in the mountainous areas in the southwest and hilly areas in the northeast have improved. From 2000 to 2020, the transfer area between WY bundle and NPP bundle is large, the area of WY bundle has decreased by 60.09%, and the area of NPP bundle has increased significantly. In 2020, it will account for 57.02% of the entire basin area. The results of this study not only help to clearly understand the spatial distribution pattern and dynamic change of ecosystem service bundles in the Huaihe River Basin, but also lay a foundation for exploring sustainable ecosystem management and planning decisions in the Huaihe River Basin.