System identification method proposed by the authors to estimate the dynamic characteristics of a building itself, under an imaginary fixed base condition in the other words, is studied for buildings with large soil-structure interaction(SSI) effect. The applicability of the method to buildings with embedment is studied in this paper. The assumed system model for the method is slightly different from the actual SSI system. This difference as well as the additional input to the underground wall may produce some system identification error. For these reasons, the proposed method and other spectral analysis procedures as well as the ARX method are applied to the response of an analytical model and results are compared. The benefit of the use of such model response instead of actual measured data is that the causality is very clear. In result, relative merits and demerits of the methods, cause and mechanism of them become clear. Furthermore, the applicability of the proposed method is confirmed. Such a method can be used to check the change of dynamic characteristics of the buildings after large earthquakes or long - term service.