BackgroundChinese medical doctors have experienced unprecedented challenges over the past 10 years, including but not limited to heavy workload and violence against doctors. In the meantime, the National Health and Family Planning Commission issued guidelines for standardised medical training that include an additional 2–4 years of specialist training for junior doctors. Few studies have explored the relationship between burnout and associated factors at Chinese medical schools and hospitals. MethodsThe study population consisted of 3387 medical students (n=2097) and residents (n=1290) from all over China. In 2016, 85 medical schools and their teaching hospitals participated in this study. We used the following questionnaires: Chinese version of the Maslach Burnout Inventory; Job Content Questionnaire; Professionalism Assessment Scale; Moral Distress Questionnaire; Jefferson Scale of Physician Empathy—Student Version; Chinese version of the General Health Questionnaire; Center for Epidemiologic Studies Depression Scale (CES-D); Professional Role Formation Inventory including sections related to lifelong learning, humanism, social learning, and research advancement; and other social demographic questions to collect cross-sectional data. Statistical analyses were conducted using SPSS 20. Ethical approval was obtained by the Institutional Review Board of the principal investigator's institution. FindingsThe burnout mean scores were 11·42 (SD 6·25) for emotional exhaustion, 8·10 (4·85) for cynicism, and 21·08 (8·70) for reduced personal accomplishment. Statistically significant increases were found as age increased and between residents and medical students (p<0·001). Higher burnout scores were significantly associated with lower empathy (p<0·001), lower professionalism (p<0·001), lower general health (p<0·001), depression (p<0·001), lower humanism (p<0·001), lower social learning (p<0·001), and lower research advancement (p<0·001)). InterpretationBurnout affects not only the physical and mental health of future Chinese doctors but also their empathy, professional role formation, and professionalism. Given China's aging population and high disease burden, educators and policy makers should not ignore burnout, wellbeing, and their effects on future doctors. FundingROC Ministry of Science and Technology Grant MOST 105-2511-S-010-002-MY2. The funding source had no involvement in study design, data collection and analysis, interpretation of the results, writing of the report, and the decision to submit the paper for publication.