Diagnosis and differential diagnosis of Inflammatory Bowel Disease (IBD) remains challenge since the particularity of small bowel. The objective of this study was to use the contrast enhanced MRI (CE-MRI) radiomics to distinguish subtypes of IBD patients. A total of 216 patients confirmed by pathology underwent small bowel CE-MRI. After the pipeline of radiomics, it was found that wavelet transformed texture features can effectively identify ulcerative colitis (UC) and Crohn’s disease (CD) with high performance. This work provides more detailed and microscopic details for the differential diagnosis of IBD subtypes based on the preliminary results.