Objective：The aim of this study was to assess the disorder of psychopsychological and vagus nerve function in patients with Crohn’s disease(CD)and analyze the relationship with clinical characteristics of CD patients so as to provide evidence for the comprehensive treatment of CD. Methods：A total of 124 CD patients were enrolled in the First Affiliated Hospital of Nanjing Medical University between January 2014 and December 2018. 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 nerve function was evaluated by heart rate variability (HRV)in 48 CD patients and 17 healthy controls. High frequency(HF)，low frequency(LF)，LF/HF and HF/(HF+LF)were analyzed. Pearson correlation analysis，Spearman correlation analysis and ordinal logistic regression analysis were used to analyze the possible link among the incidence of anxiety and depression，vagus nerve function and clinical features of CD patients. Results：Among the 124 CD patients，the incidence of anxiety and depression was 42.7%(53/124)and 27.4%(34/124)，which was significantly higher than that in the control group[8.7%(9/104)and 16.3%(17/104)]，P value were＜0.001 and 0.046 respectively. Perianal surgery history(OR= 5.405，95%CI：1.213~24.085，P=0.027)and frequency of recurrence≥2(OR=3.887，95%CI：1.242~12.166，P=0.020)were positive factors for the escalation of anxiety grades. 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 factors for the escalation of depression grades. The average value of HF/(LF+HF)of CD patients was 0.490±0.151，which was significantly lower than that of control group(0.661±0.092， P＜0.001). Vagal activity had negative correlation with symptom of anxiety(r=-0.377，P=0.008)and depression(r=-0.350，P=0.015). Conclusion：CD patients had increased incidence of anxiety and depression and showed vagus nerve dysfunction. The function of vagus nerve had negative correlation with severity of anxiety and depression in CD patients.