The fault mathematical model of the transmission of wind energy conversion system is established, and adaptive fault diagnosis observer is constructed in the presence of unknown disturbance, it can detect the faults of the system, and adaptive estimate this fault. Then, based on fault diagnosis observer, an initiative tolerant controller is designed to ensure the stability of the transmission of wind energy conversion system in case of the fault. The detail proof of stability for the system is given. The simulation results of different fault types of main transmission chain show the effectiveness and feasibility of adaptive fault diagnosis and initiative tolerant methods.