The box system that consists only of reinforced concrete walls and slabs we adopted in many high-rise apartment buildings recently constructed in Korea. Recently, many of the box system buildings with pilotis has been constructed to meet the architectural design requirements. This structure has abrupt change in the structural properties between the upper and lower parts divided by transfer girders. For an accurate analysis of a structure with pilotis, it is necessary to have the buildings modeled into a finer mesh. But it would cost tremendous amount of computational time and memory. In this study, an efficient method is proposed for an efficient analysis of buildings those have pilotis with drastically reduced time and memory. In the proposed analysis method, transfer gilders are modeled using super elements developed by the matrix condensation technique and fictitious beams are introduced to enforce the compatibility conditions at the boundary of each element. The analyses of example structures demonstrated that the proposed method used for the analysis of a structure with pilotis will provide analysis results with accuracy for the design of box system buildings.