Abstract: With advanced level of medical care and constant improvement of information technology, various medical data are rapidly accumulating. The outstanding performance of deep learning in image recognition, speech recognition and natural language processing brings new ideas for utilizing medical big data. This paper introduced the regular network structures of deep learning, reviewed the latest research progresses of deep learning in medical images, electronic medical records and genomics, and analyzed the challenges of applying deep learning in medical big data, so as to give references for applying deep learning methods in medical big data.