A blended teaching mode is necessary to improve the study efficiency of nursing students. This study aimed to explore the effects of the use of case-based learning (CBL), involving microlectures and flipped classroom teaching methods (flipped CBL mode), via online tools on the teaching of physiology to nursing undergraduates. A total of 207 nursing undergraduates were divided into a control group and a flipped CBL group. The control group received lecture-based learning, while the flipped CBL group received flipped CBL. The results showed that the final exam scores of the flipped CBL group were higher than those of the control group. The majority of nursing students believed that the flipped CBL model could provide guidance for future clinical practice, and could help in their study of physiology. Thus, the use of flipped CBL mode may improve the quality of teaching of physiology and enhance the comprehension and clinical thinking skills of nursing students.