Accurate fault prediction of rolling bearing can predict the operation condition in advance, which is an important means to ensure the safety and reliability of rotating machinery. Aimed at the data processing of rolling bearing vibration signal with multi-fault and long time series, an intelligent fault prediction model based on gate recurrent unit and hybrid autoencoder is proposed in this paper. Firstly, vibration signals of multi-faults are brought into multi-layer gate recurrent unit model for multi-step and multi-variable time series prediction. Secondly, variational autoencoder is used for data augmentation of fault samples. Thirdly, the augmented fault samples are brought into stacked denoising autoencoder for noise reduction and fault prediction. Finally, fault prediction results of rolling bearing can be achieved on the basis of gate recurrent unit and hybrid autoencoder of variational autoencoder and stacked denoising autoencoder. The bearing datasets of Case Western Reserve University are used to verify the effectiveness of the proposed method. Comparative experiment results show that the proposed fault prediction model has more accurate time series prediction result and higher fault prediction accuracy than other deep learning models. With 98.68% accuracy of fault prediction, the proposed fault prediction model can be taken as an effective tool for intelligent predictive maintenance of rolling bearing.