Abstract Virtual reality (VR) technology has significant advantages in education and teaching, on account of its strong immersive and interactive features. In this paper, based on molecular modeling tools and VR simulation, we designed a VR courseware for teaching of molecular docking, which is one of the most important computer-aided drug design technique. Voice explanation, animation demonstration, molecular visualization, interactive operation and other content were integrated in the software. Theoretical knowledge learning and VR experimental operations on molecular docking can be fulfilled in the virtual classroom. The professional terms of molecular docking are explained in simple ways to assist teaching.