Objective: To explore possible the mental health difference between freshmen upgrading from junior college and ordinary freshmen,to provide valuable reference for the targeted mental health educaiton and service. Methods: A comparative analysis of the results of University Personality Inventory (UPI) 2016-2019 among freshmen upgrading from junior college and ordinary freshmen in one university in Nanjing was carried out . Results: Among 11 955 freshmen, the detection rate of severe mental health problems (class Ⅰ) was 22.58%, scores of four indicators(physical symptoms, neurosis, depression, schizophrenia) and prevalence of class Ⅰ problems among freshmen upgrading from junior college were significantly lower than those of ordinary freshmen(P<0.05). Longitudinal comparison showed that there were significant differences in the proportion of class Ⅰ and the scores of the four indicators in each freshmen group in four years(P<0.05). After group interview with class Ⅰ, the proportion of type A and type B among freshmen upgrading from junior college were significantly higher than that of ordinary freshmen(χ2=4.12，9.23, P<0.05). Conclusion Mental health level of freshmen upgrading from junior college is higher than that of ordinary freshmen. Mental health of ordinary freshmen shows improving trend, while freshmen upgrading from junior college shows a non-linear decreasing trend,with high proportion of mental problems, which worth further attention.