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Damage assessment is one of the crucial topics in the operation of structures. Multiplicities of structural elements and joints are the main challenges about damage assessment of space structure. Vibration-based damage evaluation seems to be effective and useful for application in industrial conditions and the low-cost. A method is presented to detect and assess structural damages from changes in mode shapes. First, the mechanism of using two-dimensional continuous wavelet transform is applied for damage localization. Second, finite element model updating technique is utilized as an inverse optimization problem by applying the charged system search algorithm to assess the damage in each element sited in the first stage. The study indicates the potentiality of the developed code to assess the damages of space structures without concerning about the size and shape of structure. A series of numerical examples with different damage scenarios have been carried out in the double layer space structures and the results confirm the reliability and applicability of introduced method.