Immersive virtual reality (VR) systems are becoming widely used for education with three-dimensional (3D) information. Specifically, three-dimensional spaces to create virtual environments can help increase students’ learning interest and ability with spatial interaction. Also, with the use of multimodal interaction, VR systems can provide highly effective ways to solve problems through natural experiences. Additionally, immersive environments can bring together people in remote locations, which has been increasingly applied in education applications with the use of technology to simulate real situations. However, effective interaction methods that improve the learning ability of people participating in educational activities in 3D immersive environments are yet to be well defined. In this study, we investigated the effect of the interaction feedback types on the perception of students participating in VR environments. We conducted the experiment on three types of interaction responses, and our study was designed as a virtual chemistry class. Our experimental study showed that the interaction feedback type of a deformable object had a greater educational effect than other types of visual or audio feedback, and our results are expected to provide guidelines on how to create effective immersive education content and interaction methods.