The invention discloses a fault-tolerant power generation system for the excitation loss fault of an electric-excitation doubly salient machine, and a control method thereof. The system consists of anexcitation power circuit, an excitation power supply, a main power circuit, a main-power power supply, a controller, an energy storage capacitor, a load, an electric-excitation doubly salient machineand a position sensor, wherein the main power circuit is formed by connecting three groups of H-bridge convertors in parallel. An excitation current value is detected in real time, when an excitationloss fault is detected, the excitation power supply is cut off, the system is switched into an excitation loss fault fault-tolerant operation mode from a normal excitation operation mode, the switching tube of a main power converter is controlled to independently provide armature current required for the electric and power generation operation of the excitation loss fault so as to realize the fault-tolerant operation function of the excitation loss fault of the machine, the operation reliability of the electric-excitation doubly salient machine under various environments is improved, and thesystem is suitable to be applied to industries including aerospace, automobiles and the like.