A method for retrieving the equivalent circuit model of Frequency Selective Surface(FSS) in substrate is proposed by using the full wave numerical calculation and equivalent circuit theory. It not only has the advantage of easy physical process, but also can be applied to calculating the equivalent circuit of arbitrarily shaped FSS. In order to validate the feasibility of the proposed method, the equivalent circuit of classical square ring FSS is studied. Finally, the circular slot FSS is utilized to investigate the influence of FSS structural parameters, substrate and the angle of incident wave on the equivalent circuit parameters by the proposed method. It lays a theoretical foundation for the study of the follow-up equivalent circuit of FSS and its rapid design.