Due to the widespread availability of implicit feedback (e.g., clicks and purchases), some researchers have endeavored to design recommender systems based on implicit feedback. However, unlike explicit feedback, implicit feedback cannot directly reflect user preferences. Therefore, although more challenging, it is also more practical to use implicit feedback for recommender systems. Traditional collaborative filtering methods such as matrix factorization, which regards user preferences as a linear combination of user and item latent vectors, have limited learning capacities and suffer from data sparsity and the cold-start problem. To tackle these problems, some authors have considered the integration of a deep neural network to learn user and item features with traditional collaborative filtering. However, there is as yet no research combining collaborative filtering and content-based recommendation with deep learning. In this paper, we propose a novel deep hybrid recommender system framework based on auto-encoders (DHA-RS) by integrating user and item side information to construct a hybrid recommender system and enhance performance. DHA-RS combines stacked denoising auto-encoders with neural collaborative filtering, which corresponds to the process of learning user and item features from auxiliary information to predict user preferences. Experiments performed on the real-world dataset reveal that DHA-RS performs better than state-of-the-art methods.