Aiming at the problem of abnormal vibration of one thrust bearing test rig during the operation, the fault diagnosis of the test rig is investigated by applying dynamics and experimental method. First, based on the approach of fast Fourier transform (FFT), the vibration signal and its characteristics of the abnormal vibration are captured and extracted. Second, using the expert system fault diagnosis methods, abnormal vibration of the test rig is analyzed from three aspects: exciting force, system stiffness and resonance. Combined with the finite element calculated results, modal analysis and harmonic response analysis, it shows that the rotating frequencies are coupling with the dynamic properties, which is the vibration source of the resonance for the whole test rig. Based on this reason, three characteristics of the abnormal vibration are well explained. Finally, local optimization of the structure for the test rig is conducted. The dynamic properties of the new structure can usefully avoid the rotating frequencies. During all over the operational working cases, the resonance of the test rig will not occur. Moreover, the test results show that the new structure will not appear big vibration.