Understanding the three-dimensional (3D) structure of the human skull is imperative for medical courses. However, medical students are overwhelmed by the spatial complexity of the skull. Separated polyvinyl chloride (PVC) bone models have advantages as learning tools, but they are fragile and expensive. This study aimed to reconstruct 3D-printed skull bone models (3D-PSBs) using polylactic acid (PLA) with anatomical characteristics for spatial recognition of the skull. Student responses to 3D-PSB application were investigated through a questionnaire and tests to understand the requirement of these models as a learning tool. The students were randomly divided into 3D-PSB (n = 63) and skull (n = 67) groups to analyze pre- and post-test scores. Their knowledge was improved, with the gain scores of the 3D-PSB group (50.0 ± 3.0) higher than that of the skull group (37.3 ± 5.2). Most students agreed that using 3D-PSBs with quick response codes could improve immediate feedback on teaching (88%; 4.41 ± 0.75), while 85.9% of the students agreed that individual 3D-PSBs clarified the structures hidden within the skull (4.41 ± 0.75). The ball drop test revealed that the mechanical strength of the cement/PLA model was significantly greater than that of the cement or PLA model. The prices of the PVC, cement, and cement/PLA models were 234, 1.9, and 10 times higher than that of the 3D-PSB model, respectively. These findings imply that low-cost 3D-PSB models could revolutionize skull anatomical education by incorporating digital technologies like the QR system into the anatomical teaching repertoire.