The Hengduan Mountains (HMs), China, is a biodiversity hotspot that uplifted mainly between Late Miocene and Late Pliocene, the uplift movement might have a significant impact on the evolution of earthworms. Here, we investigated the species richness and the distribution of the earthworms in the HMs. A total of 170 species/subspecies belonging to four families and 12 genera were preliminary identified, species number in Megascolecidae account for more than 88%. Molecular phylogeny and divergence times analysis based on concatenated genes suggest that the divergence time of Moniligastridae (Outgroup) and Lumbricidae (Group 1) in the HMs was 215.84 million years ago (MYA). The divergence of first two clades in Megascolecidae (M405 and Group 2) can be date to around 44.42 MYA (95% HDP: 38.14–52.62 MYA). Dispersal of Megascolecidae from outside of the HMs to this region coincides with Indian-Eurasian collision between Eocene and Oligocene. The reconstruction of ancestral-area reveals the clades in Megascolecidae (Group 2–8) may have experienced different evolutionary histories following their divergence time during Cenozoic, which suggests that paleogeographical events might promote the dispersal and diversification of earthworm in the HMs. Unearthing the biogeographical pattern of earthworms provide insight into the evolution of soil invertebrate fauna in the temperate northern hemisphere and can be used for tracing the complex paleogeographical history of the HMs.