The floor of a car body experiences an abnormal vibration when a metro accelerates and brakes, which significantly deteriorates riding comfort. Theoretical analysis and field experiments are conducted to study this abnormal vibration, with resolution promoted and validation measurements. The short-time Fourier transform (STFT) time-frequency method is applied to tested data. It shows that the excitation of the abnormal floor vibration comes from the twice frequency of motor rotation. A mathematical model consisting of the motor shaft and gear rotor connected by a coupler is built to study the rotary dynamics of the traction system of the railroad vehicle’s powered bogie. Analysis illustrates that the dynamics in the traction system experience a shaft misalignment between the motor shaft and gear rotor. The output torque of the gear rotor is obtained and shows that this misalignment can result in even frequencies oscillation of motor shaft rotation with the twice frequency dominated. The measurement is explained by the analysis, and it is shown that the abnormal vibration can be alleviated by eliminating this misalignment. Validation measurements are conducted after eliminating the misalignment and show that the twice frequency vibration of motor rotation dropp significantly, which reduces the root mean square and amplitude of acceleration of the car body floor by 41% and 53%, respectively. The measurements agree with the theoretical analysis, and a high level of riding comfort is obtained.