The work intends to relieve the pressure on the urban medical system and reduce the cross-infection of personnel in major public health emergencies. On the premise of an in-depth analysis of the utility risk entropy algorithm model and prospect theory, the decision-making of major health emergencies is proposed. Firstly, the utility risk entropy algorithm model is optimized, and the main decision-making members are subjected to utility perception according to the perceived utility values of different levels of risk, and the weights of decision-making members are calculated and revised according to the results of utility clustering. Secondly, the prospect theory is optimized. Taking the zero as the reference point to calculate the prospect value, and taking the maximization of the comprehensive prospect value as the objective to optimize the model, the comprehensive prospect value of each scheme is calculated and sorted. Finally, the proposed scheme is tested, and the test results show that in the optimal decision-making time of the scheme, the optimal decision-making time is 0 every day. When the epidemic situation is in the first cycle, the decision-making loss of the optimal scheme is 2.69, and the reduction ratio of the optimal scheme decision-making loss is 63.96%. When the epidemic situation is in the second cycle, the decision-making loss of the optimal scheme is 0.65, and the reduction ratio of the optimal scheme decision-making loss is 94.44%. When the epidemic situation is in the third cycle, the decision-making loss of the optimal scheme is 0.22, and the reduction ratio of the decision-making loss of the optimal scheme is 89.39%. The proposed scheme can improve the processing efficiency of major health emergencies and reduce the risk of accidents.