Previous studies have found neural alterations in regions involved in cognitive and affective functions among Crohn's disease (CD) patients. The present work recruited 18 CD patients and 18 age-gender matched healthy controls (HC) and specifically compared differences in resting-state functional connectivity (RSFC) within the executive control network (ECN) which has been implicated in cognitive function and default mode network (DMN), which has been implicated in affective function. Additionally, we examined the correlations between RSFC in ECN and verbal fluency (VF) in both groups as well as RSFC in DMN and anxiety level in the CD group. Results showed significantly increased RSFC between the right middle frontal gyrus and right inferior parietal lobule in ECN, as well as increased RSFC between the right precuneus and right posterior cingulate cortex in DMN, among CD patients compared to HC. However, the correlations between ECN/DMN and behavioral scores in each group were not significant, which was possibility due to the limited sample size. These findings suggest that CD patients may experience changes in the connectivity patterns in ECN and DMN. Increased connectivity observed on these networks could be a potential biomarker of a neuropsychiatric manifestation of CD.