The invention discloses a fault-tolerant control method of a twelve-sector two-level PWM rectifier based on an equal-axis compensation ratio. The method comprises according to the position of a faultyswitch tube, determining the sectors affected by the faulty switch tube in the twelve sectors and the change of a basic voltage vector before and after the fault; determining the basic voltage vectors of each sector and the action time of the basic voltage vectors before the fault; according to the sector affected by the faulty switch, the change of the basic voltage vector and the action time ofthe basic voltage vector before the faulty switch, adjusting the action time of the basic voltage vector of the sector affected by the faulty switch; determining the on-time of the three-phase switching transistor according to the action time of the basic voltage vector and the influence of the faulty switching transistor on the sector; modulating the on-time of the switch with the triangular carrier wave, determining the PWM pulse of the switch, determining the on-off of the switch, and completing the fault-tolerant control. The invention can precisely compensate the sector where the fault occurs, and can realize the single-tube fault and the multi-tube fault.