Objective To evaluate medical students' professional cognition under the guidance of professional counselors, and to find the factors affecting the outcome of professional cognition. Methods Totally 1 111 medical students enrolled from 2018 to 2020 into Peking University Health Science Center were investigated with a self-made questionnaire. The contents of the survey included the general situation of medical students, the construction process of professional cognition and the acknowledgement of professional cognition. Chi square test and disordered multi classification logistic regression were used to analyze the influencing factors of education outcomes of professional cognition by students. Results There are 67.6% (751/1 111) of medical students had enriched their professional knowledge and understanding; 27.2% (302/1 111) of them corrected their initial understanding of the specialty; 5.2% (58/1 111) of medical students believed that the education and the role-modeling of professional counselors were completely consistent with their initial cognition. At present, the medical students majoring in the first selection of specialty at their entrance are less likely to enich and correct their original cognition (OR values are 0.301 and 0.235 respectively, all P<0.05), medical students who have frequency of contacting professional counselors are more likely to enrich and correct their original cognition (OR values are 0.000 and 0.040, respectively, all P<0.05). Conclusions The guidance of professional counselors can effectively help medical students construct professional cognition. The professional cognition of medical students is related to whether they are admitted to the first selection of specialty and whether they often meet with professional counselors.