A method based on frequency domain approaches is presented for the nonlinear parameters identification of structure having nonlinear joints. The finite element model of linear substructure is us ed to calculating its frequency response functions needed in parameter identification process. This method is easily applicable to a complex real structure having nonlinear elements since it uses the frequency response function of finite element model. Since this method is performed in frequency domain, the number of equations required to identify the unknown parameters can be easily increased as many as it needed, just by not only varying excitation amplitude but also selecting excitation frequencies. The validity of this method is tested numerically and experimentally with a cantilever beam having the nonlinear element. It was verified through examples that the method is useful to identify the nonlinear parameters of a structure having arbitary nonlinear boundaries.