Objective <p>This study focuses on the application of the flipped classroom combined with postgraduate-undergraduate collaboration (FC-PUC) teaching model in stomatological education. It aims to evaluate the impact of this integrated model on undergraduate students’ clinical operational competence, critical thinking, and learning satisfaction in stomatology courses.</p> Methods <p>A mixed-methods research approach was adopted. A total of 120 undergraduate students majoring from Hainan Medical University were randomly divided into three groups, which received traditional teaching (Lecture-based Learning, LBL), conventional flipped classroom teaching, and the flipped classroom combined with postgraduate-undergraduate collaboration teaching, respectively. By comparing the assessment scores, skill operation ratings, and student feedback across the three groups, the teaching effectiveness of the FC-PUC model was thoroughly investigated.</p> Results <p>No statistically significant difference was observed in the scores on basic knowledge questions among the three groups <i>(p &gt; 0.05</i>). In contrast, scores on case analysis questions, total theoretical scores, and the performance in three practical skills—tooth preparation for full crown restoration, pit and fissure sealing, and intraoral suturing—all exhibited a significant gradient difference (PUC-FC group &gt; FC group &gt; LBL group, <i>p</i> &lt; 0.05). The satisfaction survey indicated that, except for the dimension of rationality of class hour arrangement where no inter-group difference was found, the PUC-FC group achieved significantly higher ratings than the FC and LBL groups in other dimensions including course quality, teaching resources, and practical sessions.</p> Conclusion <p>The flipped classroom combined with postgraduate-undergraduate collaboration model significantly improves students’ operational precision, case analysis ability, and learning satisfaction. This study provides a novel pathway for optimizing stomatological education.</p>