The study of genetic admixture of nomads and farmers is significant in understanding the beginnings of the Chinese nation. Anthropology and historic research on North China give us a variety of information about human admixture and ethnic mixing in this area, and yet during this period, the impact of subsistence strategy shifts on human health is unclear. Stable isotope analysis (C & N) of human bones were undertaken from the Xitun cemetery (~200BC-580AD) located in Yanqing, Beijing, in combination with evidence from morphological study on human skeletons and historical records in order to discuss possible influences of the health of the ancient population when subsistence shifts appeared. Results show that people mostly consumed C₄-based foods during both periods, which means millet agriculture played an important role. Compared with people living during in Han Dynasty, residents in the Northern Dynasties had a higher δ ¹³C value, which could be closely related to agricultural measures implemented by governments during the ethnic mixing process. Increasing females height and changing death statistics in the Northern Dynasties indicate that development of agriculture may have had unexpected effects on people’s health. In our research, stable isotope analysis and physical anthropological methods provide a new aspect in understanding the fusion of mixing of ancient ethnic groups and thus reflect the beginnings of the Chinese nation.