The utilization of the input and output dynamic signals from multiple reference hammer impact method (MRIT) for modal flexibility extraction and structural damage identification was studied. Static and dynamic experiments on a Reinforced Concrete (RC) simply supported beam and a steel-concrete composite bridge deck were designed. MRIT was conducted on the simply supported beam and composite plate under different damage states, and modal flexibility was obtained in the test, which can be used to predict the displacement under applied loading. The beam test results demonstrated that the natural frequency decreased while the damping ratio and flexibility increased with the development of damage. Changes of natural frequency can only determine the existence of structural damage, while the changes of modal flexibility can indicate the damage location and damage degree of RC beam. Steel-concrete composite slab test results demonstrated that the differences between dynamic flexibility and static flexibility match well under the linear elastic state. Three damage cases were designed to simulate the damage situation on real bridges, which are the removal of cross diaphragm, changes of boundary condition and damage of connectors. By comparing modal flexibility information before and after structural damage, the damage of steel-concrete composite slab was achieved.