Fifteen patients with Crohn′s disease (CD) in remission diagnosed at Shanghai Jing′an District Central Hospital from February 2018 to June 2019, and 26 matched healthy subjects were recruited. All participants underwent resting-state functional magnetic resonance imaging (fMRI) scans of hippocampus. The amplitude of low-frequency fluctuations (ALFF) was calculated to determine differences in the brain. Left hippocampus was selected as seeds for functional connectivity (FC) analysis, and the results were compared between two groups. The relationship between disease duration and ALFF/FC values in abnormal regions were analyzed with Pearson correlation. Compared with the controls, the ALFF of the left hippocampus (voxel size 32) of CD patients decreased [family-wise error correstion(FWE correction), cluster level P<0.05], and the ALFF of the left medial superior frontal gyrus (voxel size 126), left supplementary motor area (voxel size 126) and left anterior cingulate gyrus increased (voxel size 37) (FWE corrected, cluster level P<0.05). Using the left hippocampus as the seed point for the whole brain functional connectivity analysis, CD patients showed increased FC strength with the left superior temporal gyrus, left medial superior frontal gyrus, left inferior frontal gyrus (opercular part), and right supplementary motor area(FEW corrected, cluster level P<0.05). Correlation analysis did not show a significantly differences between ALFF/FC value of altered brain areas and the disease duration. It suggests that there are changes in spontaneous activities and functional connectivity in the left hippocampus in patients with CD.