In order to solve the uncertain damage problem caused by measurement noise, a damage identification method based on modal strain energy mean index(MSEMI) and cloud model is presented. First, structural modal strain energy and two kinds of damage indexes are analyzed. Considering that modal strain energy dissipation ratio index (MSEDRI) and modal strain energy equivalence index (MSEEI) are complementary, a MSEMI is proposed through the mean value method. Then, some basic theories of cloud model are introduced, and numerical characteristic estimation, cloud processing algorithm and certainty function are analyzed. Finally, the damage identification method based on MSEMI and cloud model is presented to solve the uncertain damage problem. Simulation results show that the identification results of the proposed MSEMI are better than those from both MSEDRI and MSEEI, and the damage identification method based on MSEMI and cloud model can solve the uncertain damage problem caused by measurement noise.