Objective To construct a risk management model for the training of professional master's degree candidates in clinical medicine and empirically evaluate the application effect of this model in optimizing the training management process and improving training quality. Methods This study was conducted from September 2023 to October 2024 at the Second Affiliated Hospital of Harbin Medical University. A cluster sampling method was used to select 406 clinical professional master's students from the 2022 cohort trained under the traditional model (traditional management group) and 368 clinical professional master's students from the 2023 cohort trained under the education failure mode and effects analysis (EFMEA) management model (EFMEA quality control group) as the study subjects.Based on failure mode and effects analysis and the characteristics of professional master's training, an EFMEA management model was constructed following a cycle of ″risk anticipation, quantitative assessment, precise intervention, dynamic adjustment, and outcome validation.″Wilcoxon rank-sum test and Chi-square test were used to analyze the relevant data. Results The EFMEA management model identified 23 potential failure modes in the traditional management model and pinpointed 8 high-risk items. Compared with the traditional management group, the total risk priority number (RPN) value of the EFMEA quality control group was significantly reduced from 566.78 to 167.24, with a decrease of 70.5%. The pass rate for the skills exam of the Medical Licensing Examination increased from 97.3% (395/406) to 100.0% (368/368), and the pass rate for the comprehensive medical exam increased from 86.2% (350/406) to 98.4% (362/368), with statistically significant differences (all P<0.001). The professional master's candidates in the EFMEA quality control group reported a relatively high proportion of positive evaluations of the EFMEA management model, and 60.9% (224/368) of them believed that it was helpful to improve the clinical diagnosis and treatment ability. Conclusions The EFMEA management model can systematically identify and effectively reduce key risks in the training process of professional master's candidates, optimize the training management process, and help improve the training quality of clinical professional master's candidates.