Intentional cranial modification has a long history, being a ubiquitous practice in many cultures around the world for millennia. The crania excavated at the Hirota site on Tanegashima Island, Kagoshima Prefecture, Japan, has been previously noted to have a marked tendency toward a short head and a flattened occipital bone, which has been suggested to be the result of artificial cranial deformation. However, whether this deformation was intentional or caused by unintentional habits remains unclear. This study aimed to investigate the characteristics of the cranial shape of the Hirota site to clarify whether the crania were intentionally modified. In the examination of Hirota crania, Kyushu Island Jomon and Doigahama Yayoi crania were added as comparative data and contrasted with three-dimensional (3D) surface scan imaging and two-dimensional outline-based geometric morphometric analysis, combined with objective assessments of potential cranial modification. The results showcased Hirota’s short and flattened cranial morphology, indicating clear alignment with our hypothesis that Hirota samples are morphologically different from Doigahama and Jomon samples. No sex-based differences were found. Morphological abnormalities in cranial sutures were visually assessed utilizing novel 3D visualization methods of cranial outer surfaces. Based on a comprehensive review of the results, we concluded that Hirota site crania were intentionally modified. Although the motivation of the practice is unclear, the Hirota people may have deformed their crania to preserve group identity and possibly aid in the long-distance trade of shellfish, as seen archaeologically.