It is an important content of biological anthropology to explore the formation, adaption, migration and integration history of population using cranial or/and postcranial of ancient inhabitants,archeological and paleoenvironmental data. Gansu and Qinghai (or GQ) is a key area of culture and population exchange which is located in the northwest of China. Previous researches have revealed that the Neolithic -Bronze Age residents have some unique physical characteristics, and there is a certain degree of gene flow from surrounding areas. Because of limited data and partial analysis, we have no deep understanding of the variability within population, diachronic changes, and we don't know much about the extent of gene flow between Ganqing population and other groups. Through the analysis and comparative study of several craniofacial measurement data, this study discusses the population history and the diachronic changes of population based on the craniofacial variation of Gansu and Qinghai from Neolithic-Bronze Age. A total of 456 adult (male) skulls belonging to five groups are analyzed in this article,including GQ (ealier, 133), GQ (later, 110),ZY (from Central Plains, 104),XJ (from Xinjiang Province, 89) and EU (from Germany and Belgium, 20). Box plot, t-test, coefficient variation and percentiles are used to conduct this study. The results showed that: (1) From the perspective of the whole craniofacial features, the Neolithic-Bronze Age population in GQ area, is closer to that in the Central Plains; (2) The craniofacial measurement characteristics of Neolithic-Bronze Age people in GQ area have diachronic changes; (3) From the Neolithic Age to the Bronze Age in GQ region,the internal variation of the craniofacial of the population have decreased; (4) From the Neolithic Age to the Bronze Age,some craniofacial features of the ancient population in the GQ regions show a tendency which is close to that of the westerners. The climate, the subsistence strategy and gene flow have caused the changes of craniofacial morphology of ancient population in Gansu and Qinghai provinces, and the population history in this place is affected by the gene flow from Central Plains. Some features are likely to be affected by gene flow from the western and northern population.