In industrial processes, inferential sensors have been extensively applied for prediction of quality variables that are difficult to measure online directly by hard sensors. Deep learning is a recently developed technique for feature representation of complex data, which has great potentials in soft sensor modeling. However, it often needs a large number of representative data to train and obtain a good deep network. Moreover, layer-wise pretraining often causes information loss and generalization degradation of high hidden layers. This greatly limits the implementation and application of deep learning networks in industrial processes. In this article, a layer-wise data augmentation (LWDA) strategy is proposed for the pretraining of deep learning networks and soft sensor modeling. In particular, the LWDA-based stacked autoencoder (LWDA-SAE) is developed in detail. Finally, the proposed LWDA-SAE model is applied to predict the 10% and 50% boiling points of the aviation kerosene in an industrial hydrocracking process. The results show that the LWDA-SAE-based soft sensor is superior to multilayer perceptron, traditional SAE, and the SAE with data augmentation only for its input layer (IDA-SAE). Moreover, LWDA-SAE can converge at a faster speed with a lower learning error than the other methods.