Objective To analyze the learning experience of two kinds of medical online teaching videos with different organization modes by eye tracking technology, and to provide reference for the design of medical online teaching videos. Methods In December 2021, thirty-four undergraduate students majoring in five-year clinical medicine enrolled in 2019 in a medical university were selected as the research participants. They were divided into classroom record group and teacher integration group by drawing lots. The classroom recording group used video designed by the way of classroom real scene organization; the teacher integration group used video designed by virtual scene organization. Eye movement index, test scores and cognitive load test were used to compare the effect of online learning experience between the two groups. Independent sample t test was used to analyze relevant data. Results The gaze eye movement index of the students in the classroom recording group and the teacher integration group was compared: fixation time ofregion of interest (ROI) [(57.65±43.74) vs. (81.39±43.49), P=0.047], fixation times of ROI [(159.00±38.10) vs. (90.89±44.48), P=0.006], and average fixation time of ROI [(17.26±4.18) vs. 28.65±8.95), P<0.001] were lower than those in the teacher integration group, and the differences were statistically significant. The scores of theoretical knowledge test [(5.92±1.16) vs. (6.92±1.04), P=0.012] and cognitive load test [(13.47±0.94) vs. (15.76±0.97), P<0.001] of students in the classroom record group were lower than those in the teacher integration group. However, the scores of practical operation test were higher than those of teacher integration group [(7.06±1.56) vs. (5.85±1.56), P=0.031], and the differences were statistically significant. Conclusions Students have different learning experience for online video from different organization modes. The organization mode of online teaching videos should adapt to the characteristics of the teaching content and adapt to the type of courses.