This article uses the three-dimensional (3D) modeling software Maya and the 3D interactive software Unity3D to develop an interactive teaching system that integrates the display of the human brain, the display of the principle pathology of cerebral thrombosis, and the simulation of stent surgery in the brain. The use of this system can result in unlimited learning by multiple people, avoiding shortcomings such as insufficient resources, and strengthening the characteristics of interaction. For human brain models, functions such as zoom-in, rotation, and observation of a single part can be implemented, and text descriptions are provided. For the demonstration of cerebral thrombosis, animation is provided for simulation. For intra-brain stent surgery, the system can automatically demonstrate the surgical process, and it can be actually operated by the user, thereby enhancing the convenience and fun of student learning. This system uses Unity3D software as the main development tool. It uses the software’s advanced lighting system, particle system, and algorithms such as edge detection and screen post effects to establish the main frame of the system. It utilizes C # language for programming, thus enriching the functions of the system. On testing, the virtual interactive teaching system realized by the above method exhibits high interactivity, fun, and practicability.