In order to solve the problem of structural multi-damage identification, different modal strain energy damage index methods are studied and compared. First, three kinds of modal strain energy damage indices, the modal strain energy change index, the modal strain energy dissipation ratio index, and the modal strain energy based index, are described. Then, with consideration of the modal strain energy dissipation ratio index method, an improved equivalence equation is derived through improvement of the stiffness matrix, and a modal strain energy equivalence index is proposed. Finally, four kinds of modal strain energy damage indices are compared, and the impact of the measured noise is considered. Simulation results show that the modal strain energy-based index method can identify structural damage locations, and the proposed modal strain energy equivalence index can not only identify structural damage locations but can identify the damage extent with high accuracy.