In the field of physical anthropology, the physical characteristics and their development and evolution of the pre-Qin period population in the Gansu-Qinghai region have always been of great concern. Based on the cranial measurement data of the pre-Qin period populations in the Gansu-Qinghai region, this paper uses three multivariate statistical methods: discriminant principal component analysis, Euclidean distance cluster analysis to calculate the kinship among the ancient populations, and then discusses the types and development changes of the physical characteristics of the populations in this region. From the Neolithic Age to the early Bronze Age, the population in the eastern part of Gansu and the eastern part of Qinghai showed relatively uniform physical type characteristics, namely the “ancient northwest type” of the pre-Qin period. During the Bronze Age, with the southward expansion of the northern grassland bronze culture and the evolution of the population, the southern part of Ningxia presented an interlaced distribution of the “ancient northwest type” and the “ancient central plains type” populations. The eastern part of Gansu, located on the edge of the northern grassland cultural belt, also showed different characteristics of population integration.