Recently, Virtual Reality (VR) has developed rapidly. Some studies propose that VR has a great deal of potential as an instructional media for learning, while other studies indicate that VR may be ineffective or even negatively influence learners' learning experience. Few studies provide reference to educators or teachers based on empirical data. This study investigates 55 10th-grade learners' perceptions and presences in a VR-based blended learning environment. A research framework based on social presence theory and the Community of Inquiry model (CoI) was adopted in order to study social presence, teaching presence, and cognitive presence of learners in a VR-based practical, blended learning environment. The research findings are as follows: (1) VR enhanced learners' perception of the teaching equipment and the classroom, social presence, teaching presence. (2) VR-based blended learning can have a positive effect on the interest, attention, and interaction of learners. (3) For transferring well-structured knowledge, there is no significant difference between traditional instructional media and VR. But for transferring ill-structured knowledge, VR is more effective at promoting learning than traditional instructional media. In general, VR-based learning environments can positively affect students' perceptions and presence.