The invention provides a magnetic levitation display device for organic molecules and a preparation method of the magnetic levitation display device. The magnetic levitation display device comprises amounting frame, a levitation device and a demonstration device, wherein the levitation device is fixed through the mounting frame, the levitation device comprises a first diamagnetic plate, a seconddiamagnetic plate and a magnetic block, the first diamagnetic plate and the second diamagnetic plate are arranged along the horizontal direction, the second diamagnetic plate is arranged between the first diamagnetic plate and the magnetic block, and suspension space for suspension of molecular models is further reserved between the first diamagnetic plate and the second diamagnetic plate; the demonstration device comprises the molecular models and projection mechanisms, the molecular models comprise atomic models and key models connecting the atomic models, the atomic models are magnetic balls, and the adjacent atomic models are connected through the key models. The invention further provides the preparation method of the molecular models. For the magnetic levitation display device for the organic molecules and the preparation method of the magnetic levitation display device, the magnetic levitation display of the organic molecules is realized, and the construction of the three-dimensional conception of the organic molecules in chemical teaching is facilitated.