Dairy and millets have long sustained agropastoral societies in Inner Asia. While dairy pastoralism emerged across the eastern Eurasian steppe from 3000 BCE, the timing and process of its introduction into the Inner Asian mountains and integration with millet cultivation remains unclear due to the gaps in archaeological record. Here, we present the first long-term record of the integration of dairy and millet consumption in the Inner Asian mountains, based on chronological, palaeoproteomic, and stable isotope analyses of the Narensu cemetery (3050 BCE–1430 CE) in Xinjiang. This evidence reveals the earliest known convergence of Eastern and Western agropastoral technologies from 2900 BCE. Horse milk was widely consumed by 840 BCE, followed by an intensification of agrarian production during the Han–Xiongnu period. We argue that the synergy of dairy pastoralism and millet shaped a sustainable mixed economy, underpinning resilient subsistence strategies and long-term socio-ecological adaptation in Xinjiang’s diverse environments.