Aiming at solving the problems of limited training data, single input information, and limited diagnostic accuracy under the influence of strong background noise in fault diagnosis of rotating machinery, this paper proposes a fault diagnosis method based on the combination of discriminant correlation analysis (DCA) and convolutional neural network (CNN). Firstly, the original vibration signal is divided into several segments in the time domain, and the training data is directly processed by one CNN branch to extract multi-scale time domain features. Simultaneously, the divided data is subjected to discrete wavelet transform (DWT), and processed by another branch of CNN to extract multi-scale time-frequency features. Then, the DCA feature fusion mechanism is adopted to fuse the two-domain features extracted in the parallel branches to improve the model’ detection ability. Finally, the fused features are input into the deep CNN for training and learning to extract new features and output the classification results. Through the experimental analysis of two different types of data, the results show that the proposed method can be used for fault diagnosis of rotating machinery effectively. Compared with the single CNN network, the proposed method combines the multi-domain multi-scale feature extraction module with the DCA feature fusion module to enrich the feature information extraction ability. At the same time, the network performance is improved to get higher fault classification accuracy higher.