Objective: To explore the application effect of group cooperative learning combined with flipped classroom in standardized training of emergency surgery resident physicians. Methods: 95 resident physicians undergoing emergency surgery standardized training in our hospital were randomly divided into an experimental group (46, group cooperative learning + flipped classroom) and a control group (49, traditional teaching). The training period was 2 months. Results: The graduation assessment scores of the experimental group were higher than those of the control group (P < 0.05). The improvement in critical thinking ability and self-learning ability was better than that of the control group (P < 0.05). The response rate of “yes” to all items of course teaching satisfaction was significantly higher than that of the control group (P < 0.05). The satisfaction scores for training teachers were higher than those of the control group (P < 0.05). Conclusion: The teaching model of group cooperative learning combined with flipped classroom, through reconstructing the learning process and activating interactive participation, can significantly improve the clinical operation and theoretical foundation of emergency surgery standardized training students. It also cultivates core professional qualities such as critical thinking, self-learning, and team collaboration, providing a feasible paradigm for integrated medical education in this discipline.