The facial emotional information of patients is one of the important indicators of their health status. By combining facial emotion recognition technology, medical imaging intelligent diagnostic systems can more comprehensively understand the psychological and physiological status of patients. This study first selected medical imaging datasets from the publicly available Medical Machine Learning Image Standard database and performed necessary preprocessing, including data cleaning, enhancement, and standardization. Next, a CNN model is constructed to extract key features from medical images and facial expression images through structures such as convolutional layers, activation functions, pooling layers, and fully connected layers. In addition, the system also integrates facial emotion recognition module and medical image analysis module, improving the comprehensiveness of diagnosis through feature fusion. Finally, the diagnostic results are displayed through a user interaction interface. Through comparative experiments, this study verified that the proposed CNN model outperforms traditional LSTM and SVM models in terms of accuracy, recall, and precision. The CNN model has shown significant advantages in medical imaging intelligent diagnosis systems, especially achieving a recall rate of 99%, demonstrating extremely high disease recognition ability. The results of this study not only provide new research directions for the field of intelligent diagnosis in medical imaging, but also lay a solid foundation for future clinical applications.