In view of food affordability and the threshold for food security, this paper has established an integrated index for assessing the vulnerability of food security in China, which is composed mainly of the balance between food supply and demand, the reserve for food security and the economic capacity for offset food demand. Six types of food security regions are identified based on the data from county-level statistics. At regional scale, China’s food security is not optimistic. Under normal conditions without the emergence of extreme disasters and decline of grain-sown areas, China’s most vulnerable areas (Type VI) account for 30.3% of the total number of counties (cities), which are unable to meet the ends by food productivity or market based measures at subsistence levels. In China, there are only 14.5% of the counties (cities) that could guarantee well-off food security through grain production (Type I) or economic measures to meet the demand by themselves (Type III). According to the different vulnerable levels of food security and its dominant forming factors, vulnerable regions of food security in China could be classified into three categories: (1) Vulnerable regions of food security dominated by natural factors (including Type IV and Type VIa), which account for 39.4% of the total number of counties (cities), mainly located in fragile ecologic zones, i.e., farming-grazing transitional zones in the marginal areas of summer monsoon, the poor hilly areas in southern China and so on; (2) Vulnerable regions of food security dominated by low ratio of grain-sown areas (including Type VIb and Type V), which account for 16.7% of the total number of counties (cities), mostly located in the developed areas in the eastern coast of China; (3) Potential vulnerable regions of food security with underdeveloped local economies (Type II), of which 57% are the main grain-surplus regions in China, mainly located in the areas of plains and basins with favorable climate.