To obtain dynamic stability of lining structure of water diversion tunnel under the 100 years beyond 1% probability earthquake condition, the three-dimensional dynamic analysis for water diversion tunnel of large hydropower station was conducted by the dynamic time history method. The distribution of plastic zone and response characteristics of the stress and the displacement and acceleration of each key position of water diversion tunnel under earthquake was obtained. It is shown that the lining structure of the diversion tunnel was subjected to forced vibration according to the excitation ground vibration. The greater the peak of ground vibration was, the greater the dynamic displacement and tensile and compressive stress of the lining structure was. The tensile and compressive stress of the upper horizontal section at the entrance among the lining of diversion tunnel was the largest. The maximum tensile stress of the lining at the entrance is 1.3 MPa. The stress of tunnel lining was asymmetry in the horizontal direction. Each tunnel was close to the side of the other tunnel, the stress value was larger, and the stress value was smaller away from the side of the other tunnel. The farther the plastic zone of the diversion tunnel was from the entrance and exit of the tunnel, the smaller the plastic zone was. The plastic area of the surrounding rock between the eight water diversion tunnels did not occur through. After the earthquake, the plastic zone was through only in the export position of eight diversion tunnels. The local position in the diversion tunnel was damage under the 100 years beyond 1% probability earthquake condition, but the whole tunnels were safe and stable.