Purpose To summarize the imaging features of inflammatory bowel diseases (IBD) with double-filling method using multi-slice CT enterography (MSCTE), and to evaluate the clinical significance of MSCTE in diagnosis of IBD. Materials and Methods MSCTE data with double-filling method of 52 patients with IBD were retrospectively analyzed. 52 IBD patients included 42 cases of Crohn's disease (CD) and 10 cases of ulcerative colitis (UC). Bowel dilatation and lesions display were evaluated. Results Among 52 patients, ileum dilated optimal in 10 cases (19.23%) and good in 42 cases (80.77%); jejunum dilated good in 21 cases (40.38%) and poor in 31cases (59.62%). Exhaustive evaluation for large bowel diseases were good in 50 cases (96.15%). The ileocecal junction displayed well in 52 cases (100.00%). Among the 42 cases of CD, 20 cases (47.62%) had lesions limited in the small intestine, 22 cases (52.38%) had lesions involved both small intestine and colon. Among 10 cases of UC, 9 cases had lesions limited in the colon, and 1 case with the terminal ileum and the colon involved simultaneously. The MSCTE findings of 52 patients included bowel wall thickening and abnormal enhancement in 52 cases, stenosis in 28 cases, increased mesenteric vascularity in 46 cases, enlarged mesenteric lymph nodes in 27 cases, phlegmon in 10 cases, incomplete intestinal obstruction in 4 cases, abscess or inflammatory masses in 7 cases, fistulas in 3 cases, perianal lesion in 12 cases, serous cavity effusion in 15 cases, sacroiliitis in 13 cases, the urinary and biliary stones in 18 cases, and hepatosplenomegaly in 9 cases. Conclusion MSCTE with double-filling method can delineate the wall lesions of small bowels and colons very well, and can also display extraintestinal lesions and complications. It obviously improves the accuracy of localization and qualitative diagnosis on IBD.