The fault tolerant topology and control strategy for a power supply of an electromagnetic stirring system with high density magnetic field are proposed to improve the reliability and stability of the system. First, the operating principle of the electromagnetic stirring system with a high density magnetic field is analyzed. Secondly, the fault-tolerant topology design of the fore-stage three-phase rectifier and the back-stage two-phase orthogonal inverter of the electromagnetic stirring power supply are respectively carried out to improve the reliability of the electromagnetic stirring power supply in the structure. A pulse reset method is proposed. It combines with the respective control methods of the front and back stages to form a fault-tolerant control strategy, so that the fault-tolerant electromagnetic stirring power supply does not need to convert the control algorithm before and after the fault to improve the reliability of the electromagnetic stirring power supply in the control algorithm. The correctness of the fault-tolerant electromagnetic stirring power supply topology and its fault-tolerant control strategy are verified by simulation and experimental results. This work is supported by National Key Research and Development Program of China (No. 2016YFB0601302).