Accurate identification and effective control of food security risks are crucial for national security. This study constructs a food security risk system that comprises nine major types of risk sources from the perspective of the entire industrial chain. Our research identifies seven main risks that China's food security faces at the new stage: relatively lagging breeding technologies, prominent contradiction between resource supply and demand, frequent disasters, significant decline in farmers' willingness to grow grains, increased uncontrollability of market trade, inadequacy in policy compliance and stability, and frequent impacts of unexpected events. Based on this, a strategic concept is proposed, that is, a food security risk management and control system that combines early identification, normal monitoring, and emergency warning and is capable of entire industrial chain risk identification, whole-process management, and multi-level linkage. Furthermore, the following strategies for controlling food security risks are proposed: (1) promoting food security legislation, (2) launching a key scientific and technological project for constructing a national food security risk control system, (3) improving infrastructure and defense systems, and (4) optimizing market-oriented means and tools for risk management. The research results are expected to provide decision-making references for promoting the modernization of China's food security governance system and capacities.