This study aims to understand the status of depression and anxiety among Chinese university students through epidemiological investigation of a large sample size and provide a foundation for identifying individuals at risk of psychological crisis and developing targeted intervention strategies. Survey participants were selected using a multi-stage sampling approach, which incorporated elements of stratification and cluster sampling. The main participants consisted of 49,717 university students from 106 Chinese universities. Self-report questionnaires were used to assess depression and anxiety levels retrospectively. Of the 49,717 questionnaires collected, 41,620 were deemed valid after a rigorous data cleaning process, resulting in a validity rate of 83.7%. Among the respondents, 58.6% were female. The detection rates for depression, anxiety, and comorbidity of depression and anxiety among the students were 9.8%, 15.5%, and 6.5%, respectively. The detection rate of depression varied across different grades (V = 0.119) and locations of universities (V = 0.117). There were great differences in the detection rate of depression and anxiety symptoms among university students in terms of physical health (including self-rated health and vision) and health behaviors (including sleep, smoking and drinking), and physical health and healthy behaviors were important factors in the detection rate of depression and anxiety symptoms among college students. Psychological health issues among Chinese university students are relatively severe, with higher grade students exhibiting particularly concerning signs.