This paper examines changing subsistence practices from the Neolithic to the Early Han Dynasty across diverse cultural regions of China. Using a large corpus of stable isotopic data from the literature (N (human) = 3492; N (animal) = 2919), we trace spatial and temporal shifts in staple crop use and livestock management. Isotopic evidence reveals marked regional variation in crop-livestock integration from the Neolithic through the Bronze Age. During the Early and Middle Neolithic, isotopic evidence indicates pig husbandry based on the C-4-plant millet was primarily confined to the Middle Yellow River region, contrasting with an extensive pig management system in the West Liao River and Shandong regions predominantly based on C-3-plants. From similar to 5.5 ka BP, millet agriculture and pig husbandry diffused into the eastern Qinghai-Tibet Plateau, the Hexi Corridor, and western Sichuan. Despite the rapid and widespread adoption of millet agriculture in these agriculturally marginal zones, the overall utilization of pigs and the exploitation of millet-based pig feeding practices remained restricted, especially during the Bronze Age. After 5 ka BP, the introduction of non-native domesticates-such as sheep, goats, cattle, wheat, and barley-gave rise to two distinct agropastoral trajectories between the core agricultural zones and peripheral regions of northern China. In the Middle Yellow River region, an intensive agricultural system based on millet cultivation and pig husbandry persisted, with cattle and sheep rapidly integrated into existing fodder regimes but remaining supplementary to the dominant economy. By contrast, the arid northwestern regions underwent a significant shift toward a mixed agropastoral economy centered on C-3 crops (e.g., wheat and barley) and ruminant livestock, particularly sheep/goat. These regional differences highlight how local ecologies and resource availability shaped flexible but regionally distinct trajectories of crop and livestock integration in prehistoric northern China.