Objective: To investigate the mental health and influencing factors of college students during online learning under the coronavirus disease 2019 (COVID-19) epidemic, and to provide a scientific basis for mental health education. Methods: From June to July 2020, a cluster sampling method was used to select one medical and non-medical colleges and universities in southern Anhui Province. Among them, the Depression Anxiety and Stress Scale-21 (DASS-21) was used to conduct an online questionnaire survey among 3 781 medical and non-medical college students. Results: The reporting rates of depression, anxiety and stress among medical college students (30.03%, 31.05% and 14.50%, respectively) were lower than those of non-medical college students(44.49%, 46.22%, 24.81%)(χ2=81.49, 88.26, 63.08, P<0.05). During the online learning period of college students, the depression and anxiety were mainly moderate(18.43%, 20.68%), and the stress was mainly mild and moderate(9.41%, 5.29%). Multivariate Logistic regression analysis showed that non-medical students, poor parent relationships, poor relationships with fathers, teachers inadequate preparation before class, and dissatisfaction with online teaching results were prone to depression(OR=1.84, 1.28, 1.63, 1.75,1.24), anxiety (OR=1.79, 1.22, 1.65, 1.77, 1.19) and stress(OR=2.09, 1.41, 1.58, 1.29,1.48)(P<0.05). Girls were less prone to depression (OR=0.82) and anxiety(OR=0.74); College students who live in rural areas were more likely to have anxiety symptoms(OR=1.27); Senior students were more likely to feel stress(P<0.05). Conclusion The detection rate of depression, anxiety and stress negative emotion in college students was higher during online study. Families and schools should pay attention to the mental health of college students during online learning, and provide targeted psychological counseling for different students.