With the continuous development and innovation of information technology, virtual reality (VR) has become an important topic of education technology in recent years. VR is not only applied in many industries, but is also used by scholars for education applications as it enables students to have an immersive learning experience to enhance their learning effectiveness and motivation. Therefore, this study combined the spherical video-based virtual reality (SVVR) and a hands-on activity to help fifth-grade students learn natural geomorphological knowledge. The experimental group students used the hands-on approach to design a SVVR system to learn natural geomorphological knowledge; the control group used the conventional SVVR guiding system to learn. From the experimental results, there were non-significant differences in the learning achievement and learning motivation of students in the experimental and control groups. However, the students in the experimental group had better achievement on the in-depth knowledge test. In other words, the experimental group students needed to understand more about the learning content of natural geomorphological knowledge to design the VR system. Moreover, the hands-on approach cultivated their problem-solving and metacognitive skills.