To obtain the floor response spectrums and design spectrums of museum before and after isolation and perform seismic protection design for accessory structure, two finite element models of seismic non-isolated and isolated museums were established and verified through environment vibration tests. Seven seismic motions were selected, and the difference between floor waves and seismic waves was analyzed through peak acceleration and frequency spectrum. Taking the floor waves as the input, the floor acceleration response spectrums before and after isolation were calculated through MATLAB. The design spectrums were fitted according to the theory of seismic design spectrum. The results show that the dynamic characteristics of finite element model(FEM) are in a good agreement with test values.The peak acceleration of isolated structure is about 75% lower than that of the non-isolated structure. The predominant frequency of floor waves is the natural frequency of structure, which is mainly controlled by the main structure.The floor acceleration response spectrums are the results of earthquake working together with structure,which reflects the characteristics of both.The floor acceleration design response spectrums and mathematical formulas are obtained and divided into different sections before and after isolation. The non-isolated design response spectrum has 1 flat and the isolated design response spectrum has 2 flats. The research results of the design spectrum can be used in the seismic protection design of the accessory structures in different structures.