To analyze the reasons for rail clip fracture, the characteristics of rail corrugation were first measured using a rail corrugation meter. The vibration acceleration of the fastener clips at the sections with/without rail corrugation was measured, and the effects of rail corrugation on the clip vibration were analyzed. After this, a vehicle--track coupling dynamic model and a refined model for the fastener system were established in order to study the effects of rail corrugation on the vibration acceleration and stress on critical points. Finally, the rail grinding limits were determined based on the fatigue analysis method and the damage accumulation theory from the aspect of the fatigue life of the clip. The results of the study showed that the main wavelength of rail corrugation at the rail clip fracture section was approximately 40 mm. The vibration acceleration of the clip caused by rail corrugation was too large. Under normal installation conditions, the maximum clip stress was 1490 MPa at the small circular arc on the rear arch, which was identical to the on-site fracture location. The intrinsic frequency of the clip was approximately 810 Hz. Rail corrugation excited and triggered the forced vibration of the clip, and induced resonance at a speed of 120 km/h and a wavelength of 40 mm. The large cyclic stress amplitude of the clip with rail corrugation increased from 44 MPa to 68 MPa when compared with the clip without rail corrugation. Rail clip fracture was caused by the naturally occurring resonance fatigue arising from rail corrugation. For metro lines designed with a maximum speed of 120 km/h, it was suggested to control the rail corrugation amplitudes with a wavelength of 40 mm, 50 mm, 30 mm, 120 mm and 160 mm to below 0.04, 0.08, 0.16, 0.19 and 0.2 mm, respectively, taking into account the fatigue life of the clip.