Virtual reality (VR) has a high potential to facilitate education. However, the design of many VR learning applications was criticized for lacking the guidance of explicit and appropriate learning theories. To advance the use of VR in effective instruction, this study proposed a model that extended the cognitive-affective theory of learning with media (CATLM) into a VR learning context and evaluated this model using a structural equation modeling (SEM) approach. Undergraduate students (n = 77) learned about the solar system in a VR environment over three sessions. Overall, the results supported the core principles and assumptions of CATLM in a VR context (CATLM-VR). In addition, the CATLM-VR model illustrated how immersive VR may impact learning. Specifically, immersion had an overall positive impact on user experience and motivation. However, the impact of immersion on cognitive load was uncertain, and that uncertainty made the final learning outcomes less predictable. Enhancing students' motivation and cognitive engagement may more directly increase learning achievement than increasing the level of immersion and may be more universally applicable in VR instruction.