Background: This study evaluates the effectiveness of a novel compulsory–flexible course in Postgraduate Dental Basic Research Education (PDBRE). The course was designed with a mandatory core component to ensure foundational research competencies for all students, complemented by flexible elective activities to support personalized learning. We assessed its effectiveness in improving research capabilities and student satisfaction, with particular attention to differences between clinical and research postgraduates. Methods: We conducted a comprehensive evaluation using objective academic outputs and a cross-sectional survey of 111 postgraduate students. The survey assessed multiple dimensions of the learning experience, and independent-samples t-tests were employed to compare perceptions between clinical and research postgraduate students. Results: The implementation of the PDBRE course was associated with improved research output and positive student evaluations. Clinical postgraduate students reported higher overall satisfaction (3.54), compared with 3.37 among research postgraduate students. Among the evaluated dimensions, assistance with individual research received the highest rating (3.93), whereas communication channels received the lowest score (2.89). Although research postgraduates expressed relatively lower satisfaction in certain aspects, both groups recognized the course’s contribution to research skill development and long-term academic growth. Conclusion: The hybrid compulsory–flexible model is an effective approach for enhancing research competence in dental postgraduate education. Institutions may consider implementing a curriculum that combines a compulsory foundational module with flexible elective components to accommodate diverse learning needs. This approach appears particularly beneficial for clinical postgraduate students by promoting research engagement and strengthening foundational research knowledge. © The Author(s) 2026.