Provided is a sphere magnetic levitation system having magnetic-aligning devices that magnetically align the position of a sphere levitated by electromagnets according to whether the sphere is levitated, and a method of operating the sphere magnetic levitation system. The sphere magnetic levitation system includes: a sphere; a plurality of electromagnets symmetrically positioned about the sphere and spaced apart from the sphere at equal distances; and a plurality of magnetic-aligning devices provided around the sphere, and coming into contact with the sphere or separated from the sphere by a predetermined distance according to the modes of the system. The system is operated in one mode from among: an idle mode, in which the magnetic-aligning devices are in direct contact with and support the sphere; and an operation mode, in which the magnetic-aligning devices are separated from the sphere and the sphere is levitated and rotated.