Title: DeepEnFM: Deep neural networks with Encoder enhanced Factorization Machine. Abstract: Click Through Rate (CTR) prediction is a critical task in industrial applications, especially for online social and commerce applications. It is challenging to find a proper way to automatically discover the effective cross features in CTR tasks. We propose a novel model for CTR tasks, called Deep neural networks with Encoder enhanced Factorization Machine (DeepEnFM). Instead of learning the cross features directly, DeepEnFM adopts the Transformer encoder as a backbone to align the feature embeddings with the clues of other fields. The embeddings generated from encoder are beneficial for the further feature interactions. Particularly, DeepEnFM utilizes a bilinear approach to generate different similarity functions with respect to different field pairs. Furthermore, the max-pooling method makes DeepEnFM feasible to capture both the supplementary and suppressing information among different attention heads. Our model is validated on the Criteo and Avazu datasets, and achieves state-of-art performance.