A reconstructed topology with fault diagnosis and fault-tolerant control strategy of the two-phase quadrature power supply of an electromagnetic stirring system are proposed to improve the reliability of the system. First, if the back stage inverter is faulty, the topology will be reconstructed after the diagnosed fault. The reconstructed topology with the fault diagnosis can be applied twice. Additionally, a fault pulse reset method is proposed to form a fault-tolerant control strategy, for which the high-reliability electromagnetic stirring power supply does not need to switch the control algorithm before and after the failure. The reliability of the electromagnetic stirring power supply is improved greatly. Finally, simulations and experiments verify the correctness of the electromagnetic stirring power supply fault diagnosis algorithm, reconstruction topology, and its fault-tolerant control strategy proposed in this paper.