The invention discloses a fault-tolerant type electromagnetic stirring power source system and a control method thereof. A preceding stage of the system is a three-phase controlled rectifier circuit, converting a three-phase power into a stable direct current (DC) voltage for output, and supplying power for a two-phase orthogonal inverter circuit of a later stage of the system; at a DC side, two capacitors having a same capacitance value are connected in series. The later stage relates to a fault-tolerant two-phase orthogonal inverter circuit converted from three phase, inverting a DC into an alternative current (AC), being connected to a one-phase load via two output inductors. The output inductor at the output side may restrain higher harmonic and prevent an excessive current during a short-circuit fault. When the system works normally, the later stage two-phase orthogonal inverter is a two-phase three-bridge-arm inverter circuit; when a power device in the later stage two-phase orthogonal inverter breaks down, i.e., a power switch of a certain one-phase bridge arm is short circuited or has an open-circuit fault, the fault bridge arm is disconnected, and a TRIAC is correspondingly connected to constitute a two-phase half-bridge inverter circuit, so as to maintain normal operation of the system. The reliability of the power source is improved.