A levitation system of a magnetically levitated train is provided wherein superconducting magnets are installed in a car body, and the first layer and the second layer of levitation coils are so arranged as to be in a shifted location relative to each other in the moving direction of the train. By making the levitation coils two layers and by arranging the two layers in the shifted location relative to each other in the moving direction, amplitude of higher harmonic waves is reduced to a very small level, substantially to zero.