Craniosynostosis is a type of skull deformity caused by premature ossification of cranial sutures in children. Given its variability and anatomical complexity, three-dimensional visualization is crucial for effective teaching and understanding. We developed a VR database with 3D models to depict these deformities and evaluated its impact on teaching efficiency, motivation, and memorability. We included all craniosynostosis cases with preoperative CT imaging treated at our institution from 2012 to 2022. Preoperative CT scans were imported into SpectoVR using a transfer function to visualize bony structures. Measurements, sub-segmentation, and anatomical teaching were performed in a fully immersive 3D VR experience using a headset. Teaching sessions were conducted in group settings where students and medical personnel explored and discussed the 3D models together, guided by a host. Participants' experiences were evaluated with a questionnaire assessing understanding, memorization, and motivation on a scale from 1 (poor) to 5 (outstanding). The questionnaire showed high satisfaction scores (mean 4.49 ± 0.25). Participants (n = 17) found the VR models comprehensible and navigable (mean 4.47 ± 0.62), with intuitive operation (mean 4.35 ± 0.79). Understanding pathology (mean 4.29 ± 0.77) and surgical procedures (mean 4.63 ± 0.5) was very satisfactory. The models improved anatomical visualization (mean 4.71 ± 0.47) and teaching effectiveness (mean 4.76 ± 0.56), with participants reporting enhanced comprehension and memorization, leading to an efficient learning process. Establishing a 3D VR database for teaching craniosynostosis shows advantages in understanding and memorization and increases motivation for the study process, thereby allowing for more efficient learning. Future applications in patient consent and teaching in other medical areas should be explored.