Objective To investigate imaging features of multi—slice computer tomography enterography(MSCTE) in the diagnosis of inflammatory bowel disease (IBD), and to compare with the results of the conventional colonoscopy. Methods In this study, 138 IBD patients diagnosed by pathology in our hospital were selected, among them, 98 cases were Crohn's disease (CD), and 40 cases were ulcerative colitis (UC). The MSCTE and colonoscopy imaging data of all patients were retrospectively analyzed. The features of MSCTE were analyzed and compared with those of colonoscopy. Results The MSCTE imaging showed that the incidence rate of stenosis of enteric cavity, multi-segmental lesions, density increase of mesentery, proliferation of mesenteric vascular bundle, fistula formation, sinus in CD patients were higher than those in the UC patients, while the proportion of disappearance of the colonic bands among CD patients was lower than that in the UC patients (P<0.05), no difference was found in the incidence rate of the enhancement of intestinal wall, thickeness of intestinal wall and increasing peri enteric lymph node between groups (P>0.05). MSCTE could diagnose parenchymal lesions such as disappearance of IBD colon band, thickening of bowel wall and enhancement of bowel wall, which could not be diagnosed by colonoscopy, the difference was statistically significant (P<0.05). Colonoscopy could diagnosed IBD sclera and intestinal wall ulcer, which could not be diagnosed by MSCTE, the difference was statistically significant (P<0.05). The sensitivity of MSCTE for diagnosing multisegmental lesions was significantly higher than that of colonoscopy, while colonoscopy had a higher sensitivity in diagnosing multiple polyps, the difference was statistically significant (P<0.05). The sensitivity and specificity of the diagnosis of intestinal stricture was not statistically significant (P>0.05). Conclusion MSCTE has advantages in demonstrating intestinal wall thickening, enhancement of intestinal wall and extraintestinal complications of IBD, while colonoscopy is easy to demonstrate the IBD sclera and intestinal wall ulcer.