Public health and effective risk response cannot be promoted without a coordinated emergency process during a natural disaster. One primary problem with the emergency relief chain is the homogeneous layout of rescue organizations and reserves. There is a need for government-enterprise coordination to enhance the systemic resilience and demand orientation. Therefore, a bi-level multi-phase emergency plan model involving procurement, prepositioning and allocation is proposed. The tradeoff of efficiency, economy and fairness is offered through the multi-objective cellular genetic algorithm (MOCGA). The flood emergency in Hunan Province, China is used as a case study. The impact of multi-objective and coordination mechanisms on the relief chain is discussed. The results show that there is a significant boundary condition for the coordinated location strategy of emergency facilities and that further government coordination over the transition phase can generate optimal relief benefits. Demand orientation is addressed by the proposed model and MOCGA, with the realization of the process coordination in multiple reserves, optimal layout, and transition allocation. The emergency relief chain based on government-enterprise coordination that adapts to the evolution of disasters can provide positive actions for integrated precaution and health security.