Deep learning has shown the great power in the field of fault detection. However, for incipient faults with tiny amplitude, the detection performance of the current deep learning networks (DLNs) is not satisfactory. Even if prior information about the faults is utilized, DLNs can't successfully detect faults 3, 9 and 15 in Tennessee Eastman process (TEP). These faults are notoriously difficult to detect, lacking effective detection technologies in the field of fault detection. In this work, we propose Autoencoder-assisted Feature Ensemble Net (AE-FENet): a deep feature ensemble framework that uses the unsupervised autoencoder to conduct the feature transformation. Compared with the principle component analysis (PCA) technique adopted in the original Feature Ensemble Net (FENet), autoencoder can mine more exact features on incipient faults, which results in the better detection performance of AE-FENet. With same kinds of basic detectors, AE-FENet achieves a state-of-the-art average accuracy over 96% on faults 3, 9 and 15 in TEP, which represents a significant enhancement in performance compared to other methods. Plenty of experiments have been done to extend our framework, proving that DLNs can be utilized efficiently within this architecture.