Objective To explore the application of flipped classroom+micro-course model in medical aesthetics education. Methods A total of 97 students majoring in medical aesthetics from Anhui Health College from June 2024 to June 2025 were selected as the research subjects, and they were divided into the control group (n =48) and the experimental group (n =49) according to different classes. The control group adopted the conventional teaching model, and the experimental group adopted the flipped classroom+micro-course model. The teaching effect, critical thinking ability and teaching satisfaction were compared between the two groups. Results After teaching, the scores of theoretical knowledge and operational skills in the experimental group were higher than those in the control group, and the differences were statistically significant (P <0.05). After teaching, the scores of all dimensions of students' critical thinking in the experimental group were higher than those in the control group, and the differences were statistically significant (P <0.05). The satisfaction scores of teaching method, teaching content and self-evaluation in the experimental group were higher than those in the control group, and the differences were statistically significant (P <0.05). There was no statistically significant difference in the satisfaction score of teaching teachers' sense of responsibility between the two groups (P >0.05). Conclusion The application of flipped classroom+micro-course model in medical aesthetics education can improve students' assessment scores and satisfaction with teaching, while enhancing their clinical decision-making ability.