Objective: The aim of this study was to assess incidence of symptoms of anxiety or depression with CD, to examine the vagus nerve function, and to analyze the relationship between vagus nerve function and psychologic disorders of patients with CD. Methods: A total of 124 patients with CD and 104 healthy controls were enrolled between January 2014 to December 2018 in the First Affiliated Hospital of Nanjing Medical University. A total of 104 healthy controls matched by age and sex were also included. Disease activities were evaluated by the Crohn’s disease activity index (CDAI). Anxiety and depression were assessed by Generalized Anxiety Disorder (GAD-7) and Patient Health Questionnaire (PHQ-9). Vagal activity was measured indirectly by heart rate variability (HRV). Pearson correlation analysis, Spearman correlation analysis and ordinal logistic regression analysis were used to analyze the association between vagus nerve function, the incidence of anxiety and depression and clinical features of CD patients. Results: Compared with healthy controls, CD patients were more likely to have symptoms of anxiety (42.7% vs 8.7%, P<0.001) and depression (27.4% vs 16.3%, P=0.046). By ordinal regression, perianal surgery history (OR=5.405 [95%CI 1.213-24.085]，P=0.027) and frequency of recurrence (OR=3.887 [95%CI 1.242-12.166]，P=0.020) were positive correlation factors for the increase of anxiety scores. Enterectomy surgery history (OR=5.491 [95%CI 1.356-22.243]，P=0.017) and upper GI tract involvement (OR=4.774 [95%CI 1.529-14.910], P=0.007) were positive correlation factors for the increase of depression scores. The average value of HF/(LF+HF) of CD patients was 0.490±0.151, which was significantly lower than that of the control group 0.661±0.092 (P=0.000). Vagal activity had low negative correlation with symptom of anxiety (r=-0.377，P=0.008) and depression (r=-0.350，P=0.015). Conclusions: CD patients had more incidence of anxiety and depression and showed vagus nerve dysfunction. The function of vagus nerve had low negative correlation with anxiety and depression in CD patients.