The farming-pastoral ecotone is one of the ecologically fragile areas in northern China. The poor natural conditions and backward economic conditions restricted the development of production and consumption of rural residents. Since 2000, the local government has implemented a series of ecological restoration and treatment projects, and guided farmers and herdsmen to change from an extensive production pattern to an intensive one. It has improved the regional ecological conditions and optimized the production pattern of agriculture and animal husbandry, and the food consumption structure of residents has also changed accordingly. Previous studies of food consumption lacked research of long-term consumption change, which was due to the difficulty in obtaining the household tracking survey data. Besides, there were few comparative studies between farming and pastoral areas. Taking Chifeng and Ordos as examples, we used the food consumption panel data collected through the random sampling survey, to study the food consumption types and their changes of structure and quantity in the typical farming-pastoral ecotone from 2000 to 2020. The results showed that since the implementation of the ecological projects, the food consumption types have tended to diversify,but the consumption structure has still been unreasonable of rural residents. In Chifeng, the consumption structure was dominated by grains similar to the traditional farming areas; the grain consumption was steadily decreasing, while the consumption of other food types was increasing. In Ordos, the consumption structure was characterized by high consumption of grains and meat and low consumption of fruits and vegetables, which combined the characteristics of farming and pastoral areas. The annual consumption of grains and livestock meat in Ordos fluctuated greatly, reflecting the unstable output of extensive management in traditional pastoral areas. Overall, the total food consumption in Chifeng and Ordos has continued to grow in the past 20 years, with interannual variations determined by grains and meat. By 2020, grain consumption still exceeded the dietary standard of the Chinese Food Guide Pagoda, the consumption of meat, legumes and edible oil was moderate, and the consumption of potatoes, fruits and vegetables was insufficient. Especially the consumption of dairy foods increased significantly, but it was still 20 times lower than the dietary standard. Therefore, reducing grain consumption and increasing dairy consumption were the key points to adjusting the consumption structure at present. Our results can provide a scientific basis for the adjustment of food consumption structure and the optimization of agriculture and animal husbandry in the farming-pastoral ecotone.