The origin and spread of agriculture facilitated a decline in human mobility and eventually led to a predominantly sedentary lifestyle globally, including on the Tibetan Plateau. Previous studies have proposed an evolution of prehistoric agriculture, from millet-based to barley-based farming. However, details regarding the process are vague. Here, we present diachronic changes in cropping structure from Xizang on the basis of a quantitative analysis of archaeobotanical remains from 12 sites located in southeastern Xizang. The advent of agriculture in Xizang began in the southeastern region around 4800 cal a BP and resulted in a quick spread of millet agriculture from the Hengduan Mountains to the Yarlung Zangbo River region. Subsequently, the introduction of barley and wheat in Xizang led to the transformation of millet-based farming into mixed farming after 3600 cal a BP. Eventually, around 3000 cal a BP, barley and wheat dominated across the entire Xizang with declining occurrences of millet. It took more than 600 years for barley and wheat to dominate in the Tibetan cropping system, which may reflect the time required for these exotic species to adapt physiologically to their new niche. In addition to the diachronic changes in crop farming, the ratio of barley to wheat and foxtail millet to broomcorn millet also varied at different elevations possibly due to local environmental variations and the crops’ physiological requirements.