Located on the southern edge of the Loess Plateau in Shaanxi Province, the Yuejiazhuang cemetery stands out as the northernmost burial site for Qin residents and thus holds profound significance. In this research endeavor, the craniofacial traits of human skulls unearthed from this cemetery were meticulously analyzed by employing the methodologies delineated in the “Anthropometric Manual”. Through painstaking measurement and close observation of 141 skull specimens, we successfully deciphered the craniofacial morphology characteristic of the Yuejiazhuang inhabitants. The analytical outcomes disclosed a blend of medium and high cranial forms, narrow frontal aspects, medium to wide facial configurations, medium nasal shapes, as well as medium orbital features. Notwithstanding this discovery, the morphological analysis based on multivariate statistical techniques ascertained that the Yuejiazhuang residents were affiliated with the East Asian Mongolian ethnic group. Further comparative studies were conducted with individuals from the Bronze Age by means of principal component analysis and hierarchical cluster analysis. These investigations demonstrated that the Yuejiazhuang residents exhibited closer genetic affinities with those in the central Shaanxi Plain and more remote connections with their counterparts in southern Shanxi Province. Additionally, the multivariate statistical analysis hinted at the presence of specific cranial morphological discrepancies among the populations of the Qin and Jin regions during the Warring States period. Moreover, the flexed-burial customs and the accompanying grave goods discovered at the Yuejiazhuang cemetery vividly and typically mirrored the cultural elements of the Qin Dynasty. Historical records also attest that since the mid-Warring States period, the Qin state had frequently implemented population relocation policies, transplanting inhabitants to newly conquered areas to augment political governance. By integrating these elements, it can be deduced that the principal genetic constituents of the Yuejiazhuang residents predominantly stemmed from the Qin people who migrated from the Central Shaanxi Plain during the middle to late Warring States period. The Yuejiazhuang Cemetery offers invaluable perspectives into the cultural and genetic fabric of the Qin population throughout the Warring States era. Furthermore, the practice of flexed burials and the variety of artifacts interred with the deceased at Yuejiazhuang furnish additional corroboration for the historical accounts of Qin migration and resettlement strategies. These policies were presumably part of a more extensive blueprint designed to fortify Qin’s dominion over newly acquired lands by assimilating the local populace with Qin settlers, thereby safeguarding political and social stability. The genetic evidence gleaned from the Yuejiazhuang cemetery, when combined with archaeological and historical data, paints a comprehensive tableau of population migrations and cultural amalgamation during the Warring States period. It accentuates the pivotal role of state policies in molding the demographic panorama of ancient China, especially through the migration and settlement of Qin people from the central plains to peripheral regions. This synthesis of genetic, archaeological, and historical proof enriches our comprehension of the intricate social dynamics and interactions that typified the Warring States period, spotlighting the profound impact of migration on the cultural and genetic constitution of ancient Chinese populations.