Science and technology are driving people's life changes, including education and the environment. Many scholars have attempted to import technology into the classroom to help students learn in different subjects. However, students often need assistance with unfamiliar learning approaches and learning environments. This study proposed a non-immersive virtual reality (VR) guidance system combined with a two-tier strategy to help students learn geology knowledge. Two groups of students used different learning approaches: the experimental group students were guided by the two-tier test VR guidance system, and the control group students learned with the conventional VR guidance system. According to the experimental result, the two-tier test VR guidance system not only improved the students' learning achievement in natural science, but also enhanced their learning motivation. In addition, according to the sequential results, we found that VR learning materials or environmental resources can help students answer questions and solve problems more effectively.