Geographic variation of morphology is an important topic of evolutionary biology, and research on geographic variation can provide insights on the formation, evolution, and adaptation of species and subspecies. The vertebrate skull is a developmentally and functionally complex morphological structure with multiple functions, that is susceptible to vary according to selection pressure.In this study, geographic variations in skull morphology of Batrachuperus karlschmidti from four different geographic populations (Shade, Gexi, Shangluokema, and Xinduqiao) were examined via geometric morphometrics. No significant differences were found among these populations with regard to skull size; however, significant variation was found in skull shape. The most notable shape changes are the relative sizes and positions of the frontal, maxilla, pterygoid, and vomer. Skull shape changes were not related to allometry. However, due to limitation of sample populations and size, the results of this study need to be further verified by more sample populations and individuals in the future. The results of this study contribute to our knowledge about these aspects of morphological variability in this species as well as in hynobiid salamanders.