Tunnel portal sections often suffer serious damage in strong earthquake events. Earthquake waves may propagate in different directions, producing various dynamic responses in the tunnel portal. Based on the Galongla tunnel, which is located in a seismic region of China, three-dimensional seismic analysis is conducted to investigate the dynamic response of a tunnel portal subjected to earthquake waves with different vibration directions. In order to simulate the mechanic behavior of slope rock effectively, an elastoplastic damage model is adopted and applied to ABAQUS software by a self-compiled user material (UMAT) subroutine. Moreover, the seismic wave input method for tunnel portal is established to realize the seismic input under vertically incident earthquake waves with different vibration directions, e.g., S waves with a vibration direction perpendicular or parallel to the tunnel axis and P waves with a vibration direction perpendicular to the tunnel axis. The numerical results indicate that the seismic response and damage mechanisms of the tunnel portal section are related to the vibration direction of the earthquake waves. For vertically incident S waves running perpendicular to the tunnel axis, the hoop tensile strain at the spandrel and arch foot and the hoop shear strain at the vault and arch bottom are the main contributors to the plastic damage of the tunnel. The strain is initially concentrated around the tunnel foot and spandrel, before shifting to the tunnel vault and bottom farther away from the tunnel entrance. For vertically incident S waves running parallel to the tunnel axis, very large hoop shear strain and plastic damage appear at the tunnel haunches. This strain first increases and then decreases with distance from the tunnel entrance. For vertically incident P waves running perpendicular to the tunnel axis, the maximum damage factor of the slope rock and the maximum plastic strain of the tunnel are significantly lower than for S waves. Moreover, with increasing distance from the tunnel entrance, the plastic damage to the tunnel lining rapidly decreases.