There are some differences in earthquake motion of foundations supported by different levels of mountainous buildings. And the influence of these differences on the seismic response of mountainous buildings needs to be studied. Based on the topography of Zigong observation array, four RC (reinforced concrete) frame structures supported by steeped foundations were designed in accordance with Chinese code for seismic design of buildings. The ground motions of Wenchuan earthquake of Zigong observation array were selected, and three conditions of uniform input of ground motion at upper foundation, uniform input of ground motion at lower foundation and multipoint input of ground motion were designed. The ratio of the uniform input response to the multi-point input response of the structure was defined as the difference coefficient of the seismic response of the structure. Both linear and nonlinear finite element models were developed to analyze the influence of multipoint input on the seismic response of RC frame structures supported by steeped rock foundation by comparing the differential coefficient, seismic response and failure characteristics. The results are as follows: In the analysis of linear model, for the RC frame structures with long basic period, the coefficient of difference is between 0.85 and 1.12. For structures with short basic period, the coefficient of difference is between 0.38 and 1.22. Therefore, it may be unsafe to adopt uniform input seismic design for short-period RC frame structures supported by steeped foundations; In the analysis of nonlinear model, the seismic response along the slope of RC frame structures supported by steeped foundation with both long and short periods under multi-input is obviously different from that under uniform input. And the minimum difference coefficient can reach 0.27. The failure state of the bottom floor under multi-point input is more serious than that under uniform input under the extremely large earthquake. Proper seismic strengthening should be carried out for the step part and the first floor above the sill of the RC frame structure supported by steeped foundation.