In order to research the whole seismic performance of the new indoor substation roof frame-GIS complex building, the finite element models of the conventional frame and roof frame are made. Considering the uniform up and down stiffness of the roof frame-GIS building, the seismic response of the structure system which has an upper and lower structure interaction is made. The vibration characteristics and dynamic characteristics could be concluded by the modal and time-history analysis. By comparing and analyzing these numerical results, it can be seen that the lateral stiffness and the connection node of the new indoor substation roof frame should be strengthened.