Traditional biomedical data analysis technology faces enormous challenges in the context of the big data era. The application of deep learning technology in the field of biomedical analysis has ushered in tremendous development opportunities. In this paper, we reviewed the latest research progress of deep learning in the field of biomedical data analysis. Firstly, we introduced the deep learning method and its common framework. Then, focusing on the proposal of biomedical problems, data preprocessing method, model building method and training algorithm, we summarized the specific application of deep learning in biomedical data analysis in the past five years according to the chronological order, and emphasized the application of deep learning in medical assistant diagnosis. Finally, we gave the possible development direction of deep learning in the field of biomedical data analysis in the future.