Objective To address the teaching challenges in head anatomy, including the scarcity of cadaveric specimens, limited operative space, and high procedural difficulty, we applied a self-developed virtual simulation experimental software for head anatomy to regional anatomy experimental teaching and evaluated its innovative teaching effectiveness. Methods Using our self-developed head anatomy virtual simulation teaching software, we implemented a teaching intervention through extracurricular second-classroom activities with 60 undergraduate students from the 2023 cohort of the “5+3” integrated clinical medicine program at Capital Medical University. A controlled comparative design was adopted. The control group received the BOPPPS teaching model alone, while the experimental group received a combination of the virtual simulation experiment and the BOPPPS model. The educational outcomes were comprehensively assessed through three core competency evaluations, namely anatomical structure image identification, comprehensive dissection application, and practical operation efficiency, supplemented by a questionnaire survey. Results The experimental group outperformed the control group on all three competency measures, with significantly higher scores in anatomical structure image identification, comprehensive dissection application, and practical operation efficiency. Questionnaire responses demonstrated a high level of student approval of the practical effectiveness of the virtual simulation experiment in head anatomy teaching. Conclusion Incorporating the head anatomy virtual simulation experiment into regional anatomy teaching effectively compensates for the limitations of traditional cadaver dissection. It reinforces the student-centered teaching model, enhances students’ learning interest and initiative, and expands the depth and breadth of head anatomy learning. This teaching approach promotes the cultivation of students’ comprehensive practical anatomical skills, autonomous learning competence and clinical reasoning skills, and presents promising prospects for popularization in intelligent laboratory teaching of regional anatomy.