This study examines the morphological variations within and between regional populations via geometric morphometrics of larger samples of three-dimensional data of Jōmon human crania (N = 363, including 146 females, 215 males and two unknown-sex individuals) from 97 sites to investigate the population interactions in the period, which Japanese anthropologists and archaeologists have extensively discussed. The results show that morphological variations are more pronounced within individual populations especially in the principal component one, relating to the facial width, degree of prognathism, and location of occipital areas, in contrast to the relatively smaller variations observed between different phases and geographical regions. This observation is consistent with the possibility that the population interactions of the Jōmon people had been widespread and continuous, and which has an important implication for their resilience against severe climate changes at that time: The relative stability of the Jōmon society might be sustained by their frequent interactions with various populations, as suggested by insights from relevant archaeological, ethnographic, and genetic research.