Aim Historical changes in community structure underlie modern spatial diversity patterns, but few empirical studies have focused on the variation in the community composition of fossil assemblages at large spatiotemporal scales. We wanted to investigat how the spatial differentiation of mammal communities changed in China throughout the Cenozoic in response to tectonic uplift and paleoclimatic changes and explore the timing of the emergence of the modern spatially structured faunas. Location China Time period Cenozoic (from 65 Ma to the present) Major taxa studied Terrestrial mammals Methods We used a compiled database of the distributions of fossil and extant mammals to compare the multiple-site beta diversity among families and genera within six time intervals of the Cenozoic using Sørensen dissimilarity (βsor) and Simpson dissimilarity (βsim). To investigate the timing of the emergence of the modern spatially structured faunas, we applied hierarchical clustering and non-metric multidimensional scaling ordination based on pairwise βsim among seven zoogeographical regions within each time slice. Results The multiple-site beta diversity at the family level displayed hump-shaped changes during the Cenozoic, and it peaked in the Eocene and gradually decreased towards the present. However, the genus-level multiple-site beta diversity remained rather constant throughout the Cenozoic. Pronounced variations in the relationships among the zoogeographical regions were revealed in both the cluster analyses and ordinations. The modern spatial structure of mammal faunas at the family level was broadly similar to those observed in the Pliocene and Pleistocene. Main conclusions The spatial differentiation of mammal faunas in China dates back to the Eocene and pre-dates the formation of modern topography and climate. Throughout the Cenozoic, the spatial structure of mammal faunas was reorganized by an interplay of the uplift of the Tibetan Plateau, the emergence of the monsoon system and global macroevolutionary processes. The modern relationships among zoogeographical regions at the family level were established in the Pleistocene.