This study aimed to compare the impact of the partially flipped physiology classroom (PFC) and the traditional lecture-based classroom (TLC) on students' learning approaches. The study was conducted over 5 mo at Xiangya School of Medicine from February to July 2022 and comprised 71 students majoring in clinical medicine. The experimental group (n = 32) received PFC teaching, whereas the control group (n = 39) received TLC. The Revised Two-Factor Study Process Questionnaire (R-SPQ-2F) was used to assess the impact of different teaching methods on students' learning approaches. After the PFC, students got significantly higher scores on deep learning approach (Z = -3.133, P < 0.05). Conversely, after the TLC students showed significantly higher scores on surface learning approach (Z = -2.259, P < 0.05). After the course, students in the PFC group scored significantly higher in deep learning strategy than those in the TLC group (Z = -2.196, P < 0.05). The PFC model had a positive impact on deep learning motive and strategy, leading to an improvement in the deep approach, which is beneficial for the long-term development of students. In contrast, the TLC model only improved the surface learning approach. The study implies that educators should consider implementing PFC to enhance students' learning approaches.