The invention provides a magnetic levitation operation control system. The system comprises a central operation control system, a safety control center and a vehicle-mounted control system. The central operation control system completes operation planning, real-time scheduling, route presetting and turnout control of a maglev train, generates operation parameters and transmits the operation parameters to the safety control center; the safety control center is responsible for full-line access protection, full-line traction cut off, full line turnout protection, full line driving sequence control, full line train protection, the full line automatic driving, the full line speed curve monitoring and the full line positioning functions, and distributes operation data to a traction control system, a traction cut off unit, a turnout protection unit and the vehicle-mounted control system of full line all operation partitions. The centralized and unified safety control center is adopted to replace an original independent partition operation control system of each operation partition, signals of all the operation partitions are collected to the safety control center, signal interactions between adjacent operation partitions are eliminated, signal transmission faults are reduced, and the operation efficiency of the train is guaranteed.