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In civil engineering, the joints of structures are complex, and their damage is generally hard to be detected. Due to the insensitivity of structural modal information to local joint damage, this paper presents a method based on additional virtual mass for damage identification of a semi-rigid joint in a frame structure. Firstly, the modeling of a semi-rigid is described. Secondly, the frequency response of the virtual structure is constructed, and the natural frequency of the constructed virtual structure is extracted by the ERA method. By adding multiple values of virtual masses at different positions, the natural frequency information sensitive to joint damage for damage identification is effectively increased. Based on the above theory, qualitative identification of joint damage is proposed to detect the potential damage, and identification of both damage location and its extent is presented, using natural frequency. Improved Orthogonal Matching Pursuit (IOMP) algorithm is employed to improve the accuracy of the natural frequency-based method for damage identification. At last, numerical simulation of a three-story frame is performed to discuss and to verify the effectiveness of the proposed method.