We studied the geographical variation in skull morphology of the Himalayan leaf-nosed bat, Hipposideros armiger across nine populations from South China using geometric morphometrics. We found significant differences in skull size and shape among the nine populations and found the most obvious differences between populations from Simao in Yunnan Province and from Lingshui in Hainan Province. Results of multivariate regression analysis showed that both the variation in skull size and shape were associated with the variation in climatic factors across sampling localities. With increases of mean annual temperature, mean annual precipitation and mean annual humidity, the skull increases in size. The shape of the upper jaw, teeth, masseter kinsertion and the cochlea in the skull have changed. In addition, the skull size is positively related with altitude and the skull shape is related to latitude. Our results suggest that adaptation to local ecological conditions partially promotes the geographical variation in skull morphology of H. armiger in China.