Deep Neural Network (DNN)-based physical layer techniques are attracting considerable interest due to their potential to enhance communication systems. However, most studies in the physical layer have tended to focus on the application of DNN models to wireless communication problems but not to theoretically understand how does a DNN work in a communication system. In this letter, we aim to quantitatively analyse why DNNs can achieve comparable performance in the physical layer comparing with traditional techniques and their cost in terms of computational complexity. We further investigate and also experimentally validate how information is flown in a DNN-based communication system under the information theoretic concepts.