This study explores the application and feasibility of problem based learning (PBL), integrating case based learning (CBL), and the mini clinical evaluation exercise (Mini-CEX) into the standardized training of residents in nephrology department, in order to assess their clinical skills in a comprehensive manner. This prospective study enrolled 60, three years residents majoring in clinical medicine, from June 2022 to December 2023 in Nephrology Department of Baoding No.1 Central Hospital. These participants were randomly allocated into either the combined PBL-CBL and Mini-CEX teaching group (experimental group) or the traditional lecture-based teaching group (control group). Two groups were evaluated with Mini-CEX assessments and test scores upon exit the department, followed by a questionnaire survey to measure satisfaction levels for the teachers. There was no statistically significant difference in age, sex, year of graduate school, specialty and student source between the two groups of residents upon the entering the department (P>0.05). Upon the completion, the experimental group, which received PBL-CBL and Mini-CEX teaching methods, demonstrated significantly higher scores in all aspects compared to the control group, with a statistically significant difference (P<0.01). Furthermore, compared the control group, most residents in the experimental group agreed that the PBL-CBL and Mini-CEX teaching methods improve curiosity and enthusiasm for learning (73.3%), communication and expression abilities (73.3%), self-learning abilities (80%), understanding of diseases (76.7%), and like this teaching method (86.7%). PBL-CBL and Mini-CEX may be an effective method for improving medical residents' performance and enhancing their clinical skills, which is worthy of promotion in the standardized training of the residents.