Objective To study the choice tendency of medical students in Shanghai Jiao Tong University when facing moral dilemma. Methods The choice of moral dilemma was designed in the emergency room situation and the “theme of scalpers” situation. In June 2019, a survey was conducted among 506 medical undergraduates of grade 2017 and grade 2018 from Shanghai Jiao Tong University Medical College. Results In the emergency room situation, 60.5% (293/484) of the students preferred to treat the seriously injured patients and the deontological principle; 38.0%(184/484) of the students chose to treat the moderately injured patients and preferred the principle of maximum happiness. In the “theme of scalpers” situation, 89.3% (432/484) of the students thought that money should not be involved in the proper and reasonable distribution of medical resources. Conclusions Students tend to the deontological principle, and most of them think that market activities can not exclude and replace morality.