Objective: To analyze the negative emotions of college students men who have sex with men (MSM) and associated factors, so as to provide reference for alleviating MSM anxiety and depression. Methods: A total of 198 young MSM who had homosexual sex in recent 6 months during June 2019 to June 2020 were selected. Negative emotions were assessed by using Hamilton Anxiety Scale (HAMA) and Hamilton Depression Scale (HAMD). Logistic regression analysis was used to explore the related factors of negative emotion of young MSM in school. Results: The proportion of young MSM with anxiety or depression was 42.93% ( n = 85). In the negative emotion group, score of specialty and social support rating scale (SSRS) <20 points, no publicity intervention, high number of anal sex (>2), occasional or non condom use in recent anal intercourse were 50.59%, 41.18%, 54.12%, 69.14 %, 77.64%, respectively, which were significantly higher than in the non negative emotion group (32.74%, 18.58%, 30.09 %, 47.79%, 57.52%) ( χ 2=6.15, 12.21, 5.20, 9.26, 10.11, P <0.05). Junior college, SSRS score <20, no publicity intervention, high number of anal intercourse (>2), occasional or non condom use in recent anal intercourse were positively correlated with negative emotions of young MSM in school ( OR values were 1.65, 1.14, 1.90, 2.15, 1.21, P <0.05). Conclusion Anxiety and depression are prevalent among young MSM in schools, which are closely related to educational background, SSRS score, the number of anal sex and condom use during anal intercourse.