The Mountains of Southwest China, a global biodiversity hotspot, have a unique sky island landscape with high diversity of both ancient and recent-formed species. Although their distribution patterns offer significant insights into diversification processes, the complex geological and climatic history, combined with dynamic histories of gene flow in endemic taxa, makes unraveling this history challenging. This study focuses on Asian shrew moles (genus Uropsilus), an ancient group endemic to this region with an unresolved taxonomic system. By combining phylogenomic, introgression, and demographic history analyses, we investigated the historical patterns of species diversification in this genus. We detected phylogenetic discordances among rapidly diverged lineages, driven by incomplete lineage sorting, both recent and ancient gene flow, and ghost introgression. The gene flow patterns revealed strong genetic isolation in the Hengduan Mountains region, contrasted by more extensive dispersal or connectivity in areas to its east, while suggesting potential ring-like diversification around the Sichuan Basin. Demographic history indicated that rapidly diverged lineages south of the Yangtze River exhibited significantly different responses to climatic fluctuations compared with other lineages, with the East Asian monsoon likely driving their radiative differentiation and dispersal. Our study demonstrates the impacts of mountain uplift, climatic changes, and the connectivity of sky island refugia in shaping the diverse patterns of species differentiation and their distribution.