Objective To analyze the students' learning experience and preference in the online flipped classroom teaching of physiology to provide reference for the supply of online teaching resources and the design of teaching methods.Methods From March to April 2020, totally 147 undergraduates of five-year curriculum of clinical medicine in Xiangya School of Medicine were selected as the research objects. Two questionnaire surveys about students' learning experience and preference were conducted in the first and fifth week of physiology course. The data were analyzed by paired rank sum test and paired chi-square test.Results In the two surveys, students' satisfaction scores with the online flipped classroom teaching mode was 4(3,4) and 4(4,4) ,and likability scores were 4 (3, 4), the same student's satisfaction and liking degree in the second survey were higher than those in the first survey, and the differences were statistically significant (Z=-2.513,P=0.012;Z=-2.704,P=0.007). 56.4%(79/140) and 50.0%(70/140) of the students preferred 15min mini-video, while 43.6%(61/140) and 50.0%(70/140) students preferred 45min complete video, and there was no significant difference in the video preference of the same student in the two surveys(χ²=1.641,P=0.200). It was also found that 55.7%(78/140) and 60.0%(84/140) of students preferred live lectures, while 44.3%(62/140) and 40.0%(56/140) students preferred recorded lectures in the two surveys. There was no significant difference between the two surveys on the same student's preference for different teaching forms(χ²=0.500,P=0.480).Conclusions The students have a good learning experience of the online flipped classroom teaching model of physiology course, and have different learning preferences for different length of video, video and live-broadcast courses, this result suggests that the provision of online teaching resources and the design of teaching methods should meet the needs of different groups of students.