BackgroundThe innovative closed management of universities may have influenced the physical and mental health of students during the fourth stage of the COVID-19 pandemic in China. The study aimed to assess the gastrointestinal and mental health status of students in this stage and to explore the possible risk factors and mechanisms to provide a reference for future school responses to similar stressful events.MethodA multicenter, cross-sectional survey was administered to 598 college students from 10 Chinese universities. The study used the 7-item Generalized Anxiety Disorder Scale (GAD-7), 9-item Patient Health Questionnaire (PHQ-9), Fear of COVID-19 Scale (FCV-19 S), and the Diagnostic Tendency of Functional Bowel Disease Scale (DT-FBD) to evaluate anxiety, depression, fear of COVID-19 and likelihood of being diagnose diagnosed with functional bowel disease (FBD), respectively.ResultsA total of 516 college students completed the questionnaire. The proportions of students with more severe anxiety, more severe depression, greater fear of COVID-19, and a greater likelihood of being diagnosed with FBD were 49.8%, 57.0%, 49%, and 49%, respectively. These symptoms were significantly and positively correlated with the frequency of irregular sleep and eating (p < 0.05). Students in high-risk areas were more likely to experience anxiety and depression than students in areas with low/medium risk (odds ratio [OR] = 1.90, 95% confidence interval [CI]: 1.12–3.24, p = 0.017; OR = 2.14, 95% CI: 1.11–4.11, p = 0.022). A high likelihood of being diagnosed with FBD was positively associated with the severity of anxiety and depression symptoms and fear of COVID-19 (all p < 0.001). Moreover, mediation analysis revealed the following pathway in college students: fear of COVID-19 → depression and anxiety → poor diet → likelihood of being diagnosed with FBD.ConclusionCollege students generally exhibited higher more severe anxiety and depression symptoms and psychological symptoms with a greater higher propensity likelihood of being to be diagnosed with FBD. Good lifestyle habits, especially adequate sleep and a regular diet, can alleviate these problems. In addition, appropriate psychological intervention is very important.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-16145-1.