The invention discloses a real-time control system of a magnetic suspension electric main shaft and the magnetic suspension electric main shaft. The system comprises an upper debugging machine and a control circuit; the control circuit comprises a controller, a current driving module, a current sensor and a sampling module; an input end of the current sensor is used for acquiring coil current of the magnetic suspension electric main shaft; a first input end of the sampling module is connected to an output end of the current sensor, and a second input end is used for acquiring position signalsof the magnetic suspension electric main shaft; an input end of the controller is connected to an output end of the sampling module, a parameter input end is connected to a parameter output end of theupper debugging machine, and a state output end is connected to a state input end of the upper debugging machine; and an input end of the current driving module is connected to an output end of the controller, and an output end is used for driving a coil of the magnetic suspension electric main shaft. The system can improve the control instantaneity and reliability, realizes online testing and adjustment of internal parameters thereof, and meanwhile, guarantees low cost.