Abstract: The existing mainstream medical image 3D visualization systems are difficult to support cross-platform and remote use. Aimed at this problem, based on HTML5 and Three.js framework in the WebGL standard, a stereoscopic visualization system for medical anatomy is compiled. The system realized the presentation of stereoscopic visualization of medical anatomy and supplied the functions of viewing medical model: rotation, zooming, the adjustment of color transparency and light source, the calculation of length, surface area, volume and coordinate. The results show that the web system can be used for stereoscopic visualization of lung anatomical structure. The spatial position relationship between various structures can be clearly observed from multiple angles. This system provides patients with a clear understanding of their condition and communication between doctors and patients, and can be applied in various applications and has promotion prospect.