In the system identification using finite element method (FEM), system responses of overall degree of freedoms (DOFs) are necessary. Because of the limitation of sensor and other experiment equipment, the responses of unspecified DOFs have to be contained in the design variables. This increase of the design variable makes difficult to solve the inverse problem. It is one of the solutions about the problem of limited responses that the responses of unspecified DOFs are represented by the responses of specified DOFs, using the condensation method. In the previous study, we applied iterative inverse perturbation method (IIPM) to enhance the efficiency and the solution convergence of the structural system identification problems using the condensation method. So we efficiently identify structural system through solving the optimization problem with design variables which have the same number of elements. However, if the size of problem developed to analyze practical model is increased, the number of design variables which had to be considered in solving process is extremely increased. To identify large structural system, optimization strategy to efficiently change design variables during the iteration of optimization is required. In this study, we suggest two optimization strategies which are adaptive sub-domain method and genetic concept method. Numerical examples are presented to verify the efficiency of the proposed methods and to compare with those methods.