A small private online course (SPOC) supports blended learning on a small scale, enabling students to have a more comprehensive and deeper learning experience. It also provides instructors with a flexible and feasible model to better understand the students' learning needs and to supervise students' learning behaviors. In this study, we adopted SPOC flipped classroom blended teaching in the physiology course for clinical undergraduate students of Kunming Medical University. Compared with the control group [lecture-based learning (LBL)], the SPOC flipped classroom method significantly increased the scores of students in the preclass test (65.13 ± 12.45 vs. 53.46 ± 8.09, SPOC vs. LBL) and postclass test (80.43 ± 14.29 vs. 69.01 ± 12.81, SPOC vs. LBL), which is induced by students' increased interest in self-learning. More importantly, the significant difference between the preclass scores of the two groups suggested that the video lecture-based preview is more effective than the textbook-based preview. The study indicated that the SPOC flipped classroom was effective in enhancing the examination scores of students, reflecting an improved learning efficiency and a deeper understanding of the knowledge. In summary, the flipped classroom based on SPOC improves learning outcomes compared with LBL and has a wide application in the learning of basic medical courses.