Enterprise tax risk involves many aspects. In order to accurately realize enterprise tax risk assessment, an intelligent assessment method of enterprise tax risk based on deep learning is proposed. Collect enterprise tax risk information; reasonably distinguish the same type of risk information according to category, type, and appearance; extract the correlation characteristics of enterprise tax risk assessment; use the correlation characteristics to build a deep learning enterprise tax risk assessment model; search the best parameters of the automatic encoder; build a stacked automatic encoder based on the automatic encoder; combine it with the classifier; and complete the design of enterprise tax risk intelligent evaluation model. The experimental results show that the deviation ratio of Receiver Operating Characteristic (ROC), the risk assessment index of the proposed method, is less than 0.38 as a whole. Therefore, the enterprise tax risk intelligent assessment method based on deep learning is better.