Tunnels may be damaged under earthquakes, which has been observed by many earthquake events, and the buffer layer is proposed and widely investigated as a damping measure. The rubber is considered as a qualified buffer layer material because of its small elastic modulus and super elasticity, but its high price makes it difficult to apply in practical engineering. Therefore, four types of rubber buffer layers are proposed in this study, including the common rubber buffer layer and three types of perforated rubber buffer layers (PRBL), which can reduce the seismic damage and cost of tunnels. A pseudo-static method for calculating the seismic response of tunnels under horizontal and vertical earthquake motions is proposed and verified. Based on proposed pseudo-static method, a seismic design method for the buffer layer is present, and the proposed seismic design process is used to study the seismic mitigation performance of buffer layers. The initial design of the buffer layer under earthquake action E1 is carried out by pseudo-static method, and then the seismic mitigation performance is verified through dynamic time history analysis method under earthquake action E2. The earthquake action E1 and earthquake action E2 are the earthquake actions with short and long return periods of the engineering site, respectively. The results show that the common rubber buffer layer has almost no seismic mitigation performance, and the three types of PRBLs have good seismic mitigation performance. The type IV buffer layer is strip-shaped PRBL and the holes are along the longitudinal direction of the tunnel, and it has optimal seismic mitigation performance. The effects of vertical earthquake motion and peak ground acceleration (PGA) on the seismic mitigation performance of the buffer layer are studied. The results show that vertical earthquake motion has little effect on the seismic mitigation performance of different types of buffer layers. For different PGAs, the type IV buffer layer is able to efficiently decrease the peak internal force of secondary lining. The results also prove the validity of design method.