The invention provides an intelligent fault diagnosis method based on a stack pruning sparse denoising automatic encoder and a convolutional neural network, which is called sPSDAE-CNN for short. According to the method, original input data is processed by using the stack denoising automatic encoder, and more training data is obtained by using a data enhancement method. The stack sparse pruning and noise reduction self-encoder comprises a full-connection automatic encoding network, and the characteristics extracted at the front layer of the network are used for performing the operation of the subsequent layer, which means that some new connections appear between the front and rear layers of networks, so that the information loss is reduced, and more effective characteristics are obtained; meanwhile, pruning operation is introduced, so that the training efficiency and precision of the network are improved, higher training speed and high adaptability to noise signals are achieved, and the overfitting problem of the convolutional neural network is suppressed to a certain extent; according to the method, the flight data of the quad-rotor unmanned aerial vehicle are input into the model, and high fault diagnosis accuracy is obtained under the condition of high noise interference.