Medical education paradigm has been questioned for the requirements of improving the quality and quantity of medical students. This study was to explore the efficiency of integrated-based learning (IBL) used mini-clinical evaluation exercise (mini-CEX) during physical diagnostics course. One hundred and eleven volunteered students were randomly divided into three groups: lecture-based learning (LBL), case-based learning (CBL), and IBL. Nephrotic syndrome was the teaching content. In the IBL group, students were provided the guideline and additional interpretation from the instructor about the basic knowledge related to disease as vertical integration curriculum. Their performance was evaluated by mini-CEX and theoretical examination, respectively. All subjects have completed the study. The difference of five factors (medical interview, physical examination, clinical judgment, organizational effectiveness, and competence) in mini-CEX between IBL, CBL, and LBL were statistically significant (p<0.05). Sample sizes of below, meets, and above the expectations of mini-CEX in different instructional groups were statistically significant (X[superscript 2]=17.842, p=0.001). The final exam scores in IBL group and the CBL group were significantly higher than that of LBL group (F=41.553, p=0.000). And the relationship of final exam score only in the IBL group was positive existed with medical interview (R=0.466, p=0.004), physical examination (R=0.328, p=0.048), professional attitude (R=0.366, p=0.026), and communication skill (R=0.412, p=0.011). Therefore, our study revealed the effect of IBL on the medical students' skills. It highlights IBL could improve the physical examination, organizational effectiveness, and competence and the application of basic knowledge.