Objective To evaluate the application and teaching effect of flipped classroom teaching model based on micro-video in teaching of medical functional experiment. Methods All 777 students of clinical medicine in grade 2014 and 2015 were selected as the research object, of which grade 2014 as the control group, the traditional teaching model was used, grade 2015 as the experimental group was teached by flip classroom teaching mode based on micro video. After class, all students were assessed by the same theoretical test and skill operation test, and the experimental class was evaluated by questionnaire survey at the same time. Results Compared with the control group, the classroom performance and discussion score [(27.6±1.7)vs(39.3±1.5), P<0.01], experimental report and design score [(33.4±1.3) vs (38.0 ±2.4), P<0.01] and final score [(76.5±5.0) vs (83.3 ±5.1), P<0.01] of the experimental group were lower, but the scores of the computer/theory and operation test were higher[(16.8±3.4)vs(15.2±3.5),P＜0.01],there was significant difference between the two groups. The results of the questionnaire survey showed that the proportion of students in the experimental group who accepted the five aspects was 93.61%, 91.49%, 91.49%, 89.36% and 82.97%, respectively,there was significant difference between the proportion of students who did not accept the five aspects (P＜0.01). Conclusions The flipped classroom teaching method based on micro video is applied to the course of medical functional experiment, is helpful to improve students' theoretical examination and practical operation results, improve learning initiative and experiment success rate and reduce operation time.