Echolocating bats emit echolocation calls from the mouth or nose. Bats that emit calls from the nose have oddly developed dome-shaped nasal bones, but variations in the morphology of these bones are poorly understood. This study compared trends in the morphological variations of the cranium focusing on smooth structure such as the nasal swellings and the braincase, and investigated the morphological variability correlated with ultrasound vocalizations. We newly constructed three-dimensional (3-D) skull mesh models of the two Japanese rhinolophid species Rhinolophus nippon and Rhinolophus cornutus from the Korean Peninsula, the Japanese Archipelago, and Jeju Island, and compared the variations in cranium size and shape using 3-D geometric morphometrics. Additionally, we also tested trends in two representative body size indices, forearm length and centroid size. The results indicate that forearm length and log-transformed centroid size represented different trends among local populations. The results of 3-D geometric morphometrics show a significant difference in cranium shape between the two species, and between the Jeju Island population and the Japanese mainland population of R. nippon, indicating variability in the pair of nasal swellings related to nasophonation of the echolocation call. The anterior median swelling varied within the R. nippon populations, and the posterior median swelling varied between R. nippon and R. cornutus. These findings suggest that the variability between the anterior median swelling creates different echolocation peak frequencies in local populations, and that the posterior median swellings are quite similar among local populations because of the strong functional constraint of diet and echolocation.