On the Yamanashi Maglev Test Line, the on-board superconducting magnets vibrate due to harmonic magnetic fields caused by ground coils while test vehicles are running. Excessive vibration gives rise to a large heat load to make it difficult to keep the superconducting state of the magnets. So, the authors tested the superconducting magnets for vibration characteristics under these harmonic magnetic fields by an electro-magnetic vibration simulator. In this paper the results of running tests are compared with the simulations of the electro-magnetic vibration and the analysis of vibration modes and components are introduced.