The swift heavy ion irradiation effect on bilayer graphene is investigated. The radial dose distributions of delta rays produced by bismuth ions are calculated by Monte Carlo method. The radial dose rapidly decreases with increasing the distance from the track center. The energy deposited into the lattice due to electron-phonon coupling is simulated by molecular dynamics method. By given energy to a cylindrical region, the stress accumulates in this area. And then, a pressure wave emanates outwards, which leads to the atoms in the thermal spike region escaping from the upper and lower surface in the form of clusters. As a consequence, the defect configuration is composed of a central pore with radius larger than 0.5 nm and surrounding carbon chain loops.