Objective To evaluate the application effect of flipped classroom model in the course design system of healthcare-associated infection (HAI), so as to provide scientific basis for the combination of various teaching modes in the teaching course of HAI. Methods 116 students of 5-year program in Changzhi Medical College were selected as the research objects and were randomly assigned to experimental group and control group respectively, with 58 students in each group, control group adopted traditional classroom teaching method, experimental group adopted flipped classroom teaching method. During the clinical practice, the correctness and compliance of hand hygiene (HH) implementation were observed; questionnaires were used to evaluate the satisfaction degree of flipped classroom teaching mode; teaching effect was evaluated by testing. Results Students' total satisfaction degree with flipped teaching method was 63.79%. There was no significant difference in the correct rate of HH between flipped classroom mode and traditional teaching mode (P>0.05), but there were significant differences in the compliance rate of HH (88.05% vs 47.91%), passing rate of disinfection and isolation technology (86.21% vs 48.28%), as well as passing rate of occupational exposure protection (84.48% vs 36.21%) (all P<0.05). Conclusion Flipped classroom model has a high target achievement rate in the teaching course of HAI.