A method based on frequency domain approaches is presented for the non-linear parameter identification of a structure having non-linear joints. The frequency response function (FRF) of the linear substructure, which can be calculated from the finite element method or measured by an experimental method, is used to calculate its FRFs needed in the parameter identification process. This method is easily applicable to a complex real structure having non-linear joints since it uses the FRF of the substructure. Since this method is performed in the frequency domain, the number of equations can be easily increased to as many as required to identify unknown parameters, not only by just varying the excitation amplitude but also by selecting the excitation frequencies. The validity of this method was tested numerically and experimentally with a cantilever beam having a non-linear element. It was verified through examples that the proposed method is useful to identify the non-linear joint parameters of a structure having arbitrary boundaries.