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With the growing popularity of Virtual Reality (VR), the integration of the Community of Inquiry (CoI) framework provides insights into its role in facilitating student learning in VR environments. VR offers immersive experiences and visualization of abstract concepts. However, the abundance of information in VR can be overwhelming without proper guidance, hindering students' knowledge acquisition and organization. To address this issue, a concept map-based community of inquiry (CM-CoI) framework VR system was developed for a ninth-grade Earth Science course. A quasi-experiment was conducted to investigate its impact on learning achievement, reflection tendencies, and perceptions. The experimental group used the CM-CoI-based VR system, while the control group used a conventional CoI-based VR system. The results showed that the experimental group outperformed the control group in learning achievement and reflection tendencies. Interviews revealed that students in the experimental group found the method helpful for clarifying confusing knowledge. This study demonstrates the potential of CM-CoI-based VR systems to enhance learning achievement and reflection tendencies. It informs educators on integrating VR technology and concept mapping into Earth Science education, and on enhancing students' learning experiences and outcomes.