Background With the rapid development of information technology and the digitization of medical devices, various diseases require the use of medical imaging equipment for diagnosis. At present, various medical imaging diagnostic equipment such as CT and nuclear magnetic resonance can provide two-dimensional planar images of diseases. Doctors urgently need to accurately determine the spatial location, size, geometry, and spatial relationship with the surrounding tissue. Therefore, it is very important to use computer technology to segment 3D MRI images, determine the location of lesions, and then perform 3D reconstruction. Method At present, automatic recognition and marking of brain images are displayed in two dimensions. Therefore, it is necessary to use 3D visualization technology for reconstruction. In addition, it can be combined with virtual and real, and some additional information is superimposed on the brain image for integrated display. In addition, a combination of virtual and real needs to be superimposed, and some additional information is superimposed on the brain image for integrated display. The research focus of this paper includes two main parts: disease segmentation and 3D reconstruction visualization. Firstly, the disease segmentation method based on 3D MRI brain image files was designed, and then the feature extraction and 3D reconstruction functions were designed. Thereby forming a complete process of disease region segmentation and three-dimensional reconstruction. Results This study is based on a three-dimensional MRI brain image segmentation algorithm. The algorithm is advanced in technology, high in accuracy, and can effectively identify the location of the disease. Then, this study used the Unity tool to implement a three-dimensional reconstruction and visual display program for brain image disease segmentation. Therefore, the doctor can quickly and intuitively grasp the spatial information inside the brain and the information of the lesion area. Conclusion This study uses advanced disease segmentation algorithm and the latest 3D reconstruction visualization technology to initially realize the brain disease region segmentation and 3D visualization display function based on augmented reality. It has improved the diagnostic efficiency of brain diseases and has certain practical application value. And it provides a good solution for a large number of information and data display problems.