Climatic fluctuations during glacial periods have profoundly shaped the demographic history and gene flow dynamics of many taxa. This study integrated high-throughput sequencing of 67 individuals with comprehensive genomic analyses to investigate biogeographic patterns, genetic divergence and demographic trajectories in the Opisthotropis latouchii species complex, a group of mountain stream snakes distributed across Central China. Our analyses revealed substantial genetic divergence, identifying four distinct lineages, each confined to one of the four major mountain ranges in Central China, including one previously unrecognised species. These lineages exhibited distinct demographic signatures, with population bottlenecks occurring during Quaternary glaciations. Initial isolation in the glacial refugia of the southern regions of these mountains during the Late Pliocene was followed by postglacial expansions along a northward trajectory, with further divergence along a latitudinal gradient associated with mountain distribution. Notably, the mountain ranges of Central China acted as critical refugia during glacial periods, promoting rapid speciation, and as dispersal corridors during interglacial periods, facilitating range expansion and enabling recent gene flow. These findings highlight the profound impact of Quaternary climatic oscillations on genetic structure, demographic history and gene flow patterns of these endemic taxa.