With the advancement of high-speed and lightweight vehicles, the occurrence of wheel tread wear, including wheel flats, has escalated. The resulting impact loads on axle-end components and the dynamic response of the axle cannot be overlooked. On-track tests were conducted on wheel flats to obtain wheel-rail forces, axle box vibration accelerations, and axle stresses during service. Time–frequency analysis was employed to uncover patterns of variation with speed. Additionally, a dynamic model of the high-speed train–track system was developed to replicate test conditions, investigating the characteristics of wheel–rail loads and structural elastic vibrations under high-frequency excitation for various flat sizes and higher operating speeds. The findings reveal that under wheel flats, the time-domain response of the wheel–rail system exhibits periodic impacts, while the frequency-domain shows high-frequency energy comprising multiple harmonics of the wheel rotation frequency. Wheel–rail forces, axle box vibration accelerations, and axle stresses exhibit inflection points with increasing speed, particularly within the 120–160 km/h range. In the high-frequency domain, axle stresses display characteristic frequencies that remain unchanged with speed, attributed to the coupled vertical bending vibration modes of the wheel–rail system. These research results offer foundational support for predicting fatigue damage to axle-end components, assessing axle stress, and establishing tolerances for tread defect limits.