Large-scale sudden-onset disasters may cause massive injuries and thus place great pressure on the emergency blood supplies of local blood banks. When blood is in short supply, blood products gathered urgently to a local blood center should be appropriately allocated to blood banks in the affected area. Moreover, ABO/Rh(D) compatibilities among blood groups must be considered during emergency situations. To minimize the total unmet demand of blood products considering the optimal ABO/Rh(D)-compatible blood substitution scheme, a mixed integer programming model is developed and solved efficiently by using a greedy heuristic algorithm. Finally, a numerical example derived from the emergency blood supply scenario of the Wenchuan Earthquake is presented to verify the proposed model and algorithm. The results show that considering ABO/Rh(D)-compatible blood substitution can remarkably increase the efficiency of emergency blood allocation while lowering blood shortage, and the preference order of possible ABO/Rh(D)-compatible substitutions has an influence on the allocation solution.