Virtual reality (VR) has made it possible for users to access novel digital experiences. An interesting question that arises in the context of VR is whether it appears or feels different to users when different virtual environments are used. This study investigates the effect of VR head-mounted display (HMD) and desktop computer-facilitated VR on users’ sense of presence (spatial presence and immersion) and task-oriented self-efficacy when exposed to an earthquake education VR system. A quasi-experiment design was used with a sample of 96 university students. The results revealed that the VR system had positive impacts on the users’ earthquake preparedness self-efficacy. Although the experiment group (n = 39) had repeated experiences, as they first used desktop VR followed by VR HMD for the same content, users indicated a higher sense of spatial presence and immersion while using VR HMD than when using desktop VR. In addition, a VR HMD single-group pre- and posttest experimental design was performed with 20 participants, and the differences between the pretest and posttest measurements of earthquake preparedness and self-efficacy were determined to be significant. The qualitative results reveal that the visual stimulus and motion are relevant in composing the VR experience.