The actuator and sensor system of the UAV is affected by many factors such as materials and environment, the UAV is prone to various types of faults and even may crash in severe cases. Therefore, the effective diagnosis of the early fault of the UAV is of great significance in preventing flight accidents. The paper chooses the Simulink model of the sixrotor UAV as the research object, a probabilistic neural network fault diagnosis model based on Fast Fourier transform (FFT) is proposed for the early fault of aircraft motor and angular velocity sensor. The flight control model of the sixrotor UAV is established on the Simulink platform. Then the FFT is used to analyze the data in an effective timefrequency analysis. Finally, the probabilistic neural network model is implemented with MATLAB, and the FFT data is used to classify the faults to realize fault diagnosis of UAV.