This study aims to explore approaches to integrating multiple stakeholders to participate jointly in public food safety emergency management. We analyzed the evolution and characteristics of organizational models of public food safety emergency management in China and revealed the organizational crux thereof, that is, the deficient bureaucratic model caused by fragmented management. This causes an internal bureaucratic dilemma for government supervision and triggers organizational problems in terms of environmental adaptability, plan operability, information transmission, multi-sector governance, and policy dependence of decision-making and execution. Furthermore, we proposed a three-system-integrated organizational mode and analyzed its operation mechanism from the aspects of organizational structure as well as planning, information, decision-making, and support mechanisms. The three-system-integrated model is the evolution direction for China's public food safety emergency management and will play an active role in encouraging the effective participation of diverse social subjects in social co-governance of food safety risks.