Food security and the utilization of natural resources in a sustainable manner are vital to the expansion of China's agricultural system. The relationship between environmental pressure and dietary structure has influenced the quantity and spatial distribution of China's food supply and demand, but it has not been evaluated. Our research centered on the security of China's food nutrition–resources–food (NRF) system, considering the inherent relationship between food security, nutritional health, and resource security. The following are the study's findings: (1) The Chinese population is rapidly changing from a diet focused on grains to a more diverse diet. Between 1990 and 2019, the dietary quality and nutritional status of Chinese individuals have vastly improved. In terms of nutrient levels, discrepancies between urban and rural resident persist, with urban residents consuming a diet that is closer to the ideal structure. However, the structure of rural residents' food consumption is diversifying, and the gap between urban and rural residents is gradually narrowing. (2) From 2000 to 2019, the pressure, status, and response indices of China's NRF system all show an upward trend, and the security of the NRF system has steadily grown. The magnitude of change in the response index exceeded that of the state index, which exceeded that of the pressure index. This indicates that the increase in the pressure and state indices of the NRF system was primarily attributable to the effectiveness of policy efforts.