Several studies indicated that the Hengduan Mountains acted as refugia during the Pleistocene. Complex topographic configuration in this area might have played an important role in shaping the genetic divergence. Here, we investigated the phylogeography of the Chinese white-bellied rats, Niviventer confucianus, to test the role of mountain ranges in the Hengduan Mountains. Our results revealed that N. confucianus populations were clustered into three geographic lineages, which were consistent with the geographic origin, where, the Daxueshan Mountains but not the Daocheng Ice Cap regions contributed to the genetic divergence of N. confucianus populations. The Daxueshan Mountains separated N. confucianus populations into two distinct evolutionary lineages (clade A and clade B) and Motuo population formed monophyletic group (clade C). Results from the mismatch distribution and neutrality test analysis suggested a range expansion of the two clades (clade A and clade B). Divergence time estimation indicated that all splits within each clade occurred after the mid-Pleistocene. All results revealed that the complex topographic configuration in the Hengduan Mountains contributed to the genetic divergence of N. confucianus.