Objective: To analyze the dilemmas in clinical research among Master of Chinese Medicine (MCM) students and to explore countermeasures for improving the quality of research training. Methods: A questionnaire survey was administered among MCM students at a university. The problems were analyzed from four dimensions: topic selection direction, research method, ethical consciousness, and process management. Results: A total of 40 questionnaires were distributed to MCM postgraduate students, with 36 valid responses returned, representing an effective recovery rate of 90.0%. Regarding the grade distribution of respondents: 12 (33.3%) were first-year students, 13 (36.1%) second-year, and 11 (30.6%) third-year. The survey results showed that students’ research topics were mainly focused on basic and animal experimental research, accounting for 38.9%, and most topics were proposed by supervisors or derived from research projects (44.4%). In addition, 41.7% of students reported that pressure from SCI publication requirements significantly influenced their topic selection. Insufficient mastery of clinical research methods was a prominent problem: 77.8% of students were unable to estimate sample sizes, 80.6% could not use statistical analysis software, and 72.2% had an unclear understanding of randomization. Ethical awareness was also weak. Only 22.2% of students obtained ethical approval; 33.3% recognized its role in protecting human subjects, while 41.7% regarded it merely as a procedural requirement. Open-ended responses revealed the core difficulties mentioned: heavy clinical workload (15 mentions), methodological challenges (13 mentions), and inadequate supervisor guidance (9 mentions). Key demands included methodological training (12 mentions), guaranteed research time (10 mentions), enhanced supervisor guidance (8 mentions), statistical consultation, and a simplified ethical review process. Conclusion: The clinical research of MCM students of traditional Chinese medicine is faced with the dilemma of “basic” tendency of topic selection, insufficient mastery of research methods, weak ethical cognition, and prominent contradiction between clinical and scientific research. It is urgent to strengthen methodology training, optimize time guarantee, and perfect tutor guidance.