In order to satisfy the anti-seismic requirement of Tertiary Mirror System(M3S)in a Thirty Meter Telescope (TMT), the structural responses of Tertiary Mirror Cell Assembly (M3CA) under the earthquakes with 200-year and 1000-year return periods were analyzed. Firstly, a seismic response spectrum of M3S was established by modifying the seismic response spectra of TMT according to M3S mechanical character. Then, the structure responses of displacement, stress and acceleration under different level earthquakes were analyzed. The analysis results show that the peak response appeares when the earthquake with 1000-year return periods transmits to M3S in three directions (two horizontal orthogonal and a vertical). The peak acceleration of M3CA, maximum displacement and the peak stress are 2.844g, 1.544 mm, and 552.316 MPa , respectively, moreover, the peak stress on Tertiary Mirror (M3) is 1.401 MPa. The investigation of material property indicates that the lateral support rods will be broken at this moment and the protective support for M3 is recommended. As a result of sufficient consideration of different influencing factors in spectrum analysis, the data can provide reliable references for detail designs of M3Ss.