The tradeoffs and synergies of ecosystem services are widely discussed and recognized. However, explicit information for understanding and managing the complex relationships of multiple ecosystem services at regional scales is still lacking, which often leads to the degradation of important ecosystem services due to one ecosystem service being enhanced over another. We assessed the biodiversity and the production of nine ESs (ecosystem services) across 779 counties in the Yangtze River Basin, the largest basin in China. Then, we mapped the distribution of ES for each county and used correlations and “partitioning around medoids” clustering analysis to assess the existence of ES bundles. We found five distinct types of bundles of ecosystem services spatially agglomerated in the landscape, which could be mainly explained by land use, slope and altitude gradients. Our results also show landscape-scale tradeoffs between provisioning and almost all regulating services (and biodiversity), and synergies among almost all regulating services (and biodiversity). Mapping ecosystem service bundles can identify areas in a landscape where ecosystem management has produced exceptionally desirable or undesirable sets of ecosystem services, and can also provide explicit, tailored information on landscape planning for ecosystem service conservation and the design of payment policies for ecosystem services within diverse landscapes at watershed scales.