Accurately predicting the fatigue life of fastener clips is crucial for improving material processing technology, enhancing the anti-fatigue design level, and guiding the maintenance and repair of track structures. Conventional methods that solely evaluate the fatigue life of fastener clips based on the uniaxial stress index under displacement loads may lead to significant errors. In this paper, the stress field of a type-III clip under displacement loading conditions was numerically simulated based on fatigue test standards, and the fatigue life of the clip was analyzed using the Fatemi–Socie (FS) multiaxial fatigue criterion based on the critical plane method. A comparison with standard fatigue test results revealed that, under non-resonance conditions, the predicted position of the fatigue critical plane of the fastener clip coincided with the fracture surface observed at the middle of the measured small arc, with a life prediction error of 7.3%. To further investigate the predictive capability of the FS multiaxial fatigue criterion for the fatigue life of the fastener clip under resonance conditions, the stress levels of the clip under non-resonance and resonance conditions were compared through on-site testing, and the effects of inertial loads caused by vertical and lateral vibration acceleration on the stress field of the clip were analyzed in numerical simulation according to the results of clip acceleration tests; the fastener clip’s resonance fracture position and fatigue life were also predicted based on the aforementioned multiaxial fatigue criterion. To verify the accuracy of the predicted results, a testing method was proposed that equates the high-frequency resonant inertial load of the fastener clip to a low-frequency additional preload under the premise of consistent stress fields. A comparison with the numerical simulation results shows that considering only vertical inertial loads would result in a discrepancy between the measured fracture location and the actual one. Considering both vertical and lateral inertial loads, the fracture location (at the heel of the small arc) under resonance conditions could be accurately determined, with a life prediction error of 13.8%. Compared to the non-resonant displacement loading condition, the inertial loads caused by acceleration under resonance conditions led to a reduction in fatigue life of approximately 77.8%.