The structural system of a hybrid building is composed of upper shear wall which resist lateral force by bending deformation and lower frame which resist lateral force by shear deformation. A deep transfer girder is used to transfer gravity load safely from super structures to structural frame beneath. Because of the vertical discontinuity, a building with transfer girder must be analyzed by dynamic analysis. However, this structural system has many problems in performing dynamic analysis that cannot be solved by general analysis procedure. The slabs In transfer floor are considered as either a Plate element or a rigid diaphragm in finite element analysis without appropriate evaluation of their characteristics. Therefore, a reasonable analysis method is proposed in this study by evaluating the diaphragm effect of a hybrid structure system.