Aiming at the problem that emergency decision making mostly relies on experts in the department and ignores the public, we put the public into the emergency decision making, and then propose a new multi-department large group emergency decision making method. Firstly, experts give attributes’ values of the alternatives, while the public give their preferences of the attributes. The departments choose the public clusters based on the top N rule. Then, combining the attributes’ values of the alternatives with preferences of the attributes, the total score of alternatives is got by using the method of logic scoring of preference(LSP). Furthermore, decision-theoretical rough set in two universes is introduced, and the loss values of alternatives given by experts are combined with total score of alternatives. The alternatives in positive universe are selected according to the decision rule to respond to the emergency. Finally, an example is given to illustrate the effective of the proposed method.