In Southeast and South Asia including Myanmar and Bangladesh, the house shrew (Suncus murinus) is widely distributed and consists of multiple lineages of mitochondrial DNA. However, there has been no morphometric investigation among such lineages, despite the obvious recognition of large variation in their body size and shape geographically. To elucidate morphological differences among local populations in reference to multiple lineages of S. murinus, we conducted geometric morphometrics to investigate skull morphological variations focusing on highly diverged Myanmar and adjacent Bangladesh and Vietnam populations. Our findings indicate that skull shape changes can distinguish adjacent lineages, and some individuals represent intermediate forms between the two geographically adjacent lineages. The results also represent several overlaps of skull size and allometric shape changes among Myanmar populations, suggesting the presence of intermediate individuals due to hybridization. Additionally, allometric shape changes were observed in the sites of attachment of muscles or tendons between the cranium and the mandible suggesting an association with piecing or decaying soils and woods. Our findings provide fundamental insights into the skull morphological features of S. murinus, which contributes to a more comprehensive understanding of the evolutionary processes of morphological variation in the house shrew.