Objective To explore the relationship between cognitive level of doctor-patient relationship and career decision-making self-efficacy among clinical medical interns. Methods The Career Decision-Making Self-Efficacy Scale and Difficult Doctor-Patient Relationship Questionnaire-10 were used for investigation among 216 clinical medical interns in Southwest China. Results No significant difference was found in the cognitive level of doctor-patient relationship between clinical medical interns of different sexes （P > 0.05）; the career decision-making self-efficacy of males was significantly higher than that of females （t = 2.459， P = 0.015）; the overall cognitive level of doctor-patient relationship and dimensions of doctor’s subjective experience and patient’s behaviors combined with doctor’s subjective experience were negatively correlated with career decision-making self-efficacy （P < 0.01）; the dimensions of doctor’s subjective experience and patient’s behaviors combined with doctor’s subjective experience in the cognitive level of doctor-patient relationship had a predictive effect on career decision-making self-efficacy of clinical medical interns. Conclusion The cognitive level of doctor-patient relationship is an important factor affecting the career decision-making self-efficacy of clinical medical interns.