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Augmented Reality (AR) is a technology that allows overlaying the computer-generated virtual information into the userpsilas view of the real world, and with changes of his position and line of sight, the virtual objects will change accordingly. AR has many potential applications in industrial operations and academic research. First, this paper discusses the development of 3D visualization of crystal molecular structure. Next, the paper addresses the design of 3D macromolecule visualization based on AR. Then, the paper discusses 3D modeling of macromolecule. 3D model of crystal molecular is built with grid modeling in OpenGL. Finally, the paper makes a verifying research on it. The data of molecular was downloaded from internet database. The AR visualization system is established in ARToolKit. The result is stable, immersive and interactive.