Objective: To explore the differences in mental health between freshmen with and without disabilities. Methods: A comparative analysis of 6 114 freshmen with and without disabilities from an undergraduate college in Nanjing from 2018 to 2020 was measured by the SCL-90 Mental Health Symptom Self Rating Scale. Results: The positive detection rate of SCL-90 was 23.29%, and the positive rate of disabled students was significantly higher than healthy students( χ 2= 28.35 , P <0.01); Disabled freshmen were significantly higher than healthy freshmen in the levels of all factors( P <0.05); A longitudinal comparison of the positive detection rate of SCL-90 between the two groups of freshmen in three years, there was no statistical difference between the disabled freshmen( χ 2=5.82, P =0.06), there was a statistical difference in healthy freshmen( χ 2=29.43, P <0.01); After interview with positive factor students, the composition ratio of freshmen with disabled of A and B was higher than that of healthy freshmen( χ 2= 7.09 , P <0.05). Conclusion Mental health level of freshmen with disabled is lower than that of healthy freshmen. Mental health among freshmen without disabilities is worsening. The mental health of disabled freshmen is relatively stable, however, the proportion of students with psychological problems is relatively high, which requires attention.