With the help of a two-dimensional particle-in-cell simulation model, we investigate the long-time evolution (near 100Ωi0−1 , where Ω i0 is the ion gyrofrequency in the upstream) of a quasi-parallel shock. Some of the upstream ions are reflected by the shock front, and their interactions with the incident ions excite low-frequency magnetosonic waves in the upstream. Detailed analyses have shown that the dominant wave mode is caused by the resonant ion–ion beam instability, and the wavelength can reach tens of ion inertial lengths. Although these plasma waves are directed toward the upstream in the upstream plasma frame, they are brought by the incident plasma flow toward the shock front, and their amplitude is enhanced during the approaching. The interaction of the upstream plasma waves with the shock leads to the cyclic reformation of the shock front, and the reformation period is slightly larger than 10 Ωi0−1 . When crossing the shock front, these large-amplitude plasma waves are compressed and evolve into current sheets in the transition region of the shock. At last, magnetic reconnection occurs in these current sheets, accompanying the generation of magnetic islands. Simultaneously, there still exist plasma waves of another kind, with the wavelength of several ion inertial lengths in the ramp of the shock, which are excited by the nonresonant ion–ion beam instability. The current sheets in the transition region are distorted and broken into several segments when the plasma waves of this kind are transmitted into the downstream, where magnetic reconnection and the generated islands have a much smaller size. No obvious ion flow can be observed around some X-lines produced in the magnetic reconnection, and this implies that electron-only reconnection may occur.