Objective To investigate the diagnostic value of capsule endoscopy and Lewis score in small bowel Crohn’s disease. Methods 119 patients suspected of small intestinal Crohn’s disease(CD)underwent capsule endoscopy in our hospital were retrospectively analyzed. They were divided into CD group and non-CD group. The manifestation of small intestinal lesions and Lewis scores were compared between the two groups. Results There were 66 cases in CD group and 53 cases in non-CD group. Lewis score was 441(191-638)in CD group,which was higher than that in non-CD group 101(56-219)(P<0.05). Longitudinal ulcer, irregular ulcer, and cobblestone appearance in CD group were higher than those in non-CD group(P<0.05). The highest specificity of CD’s diagnosis in different pathological types were cobblestone appearance, polypoid hyperplasia and longitudinal ulcer, which were 98.1%, 90.6%, and 84.9%, respectively. The highest sensitivity were irregular ulcer, Lewis score, and circular ulcer, which were 77.3%, 72.7%, and 72.2%, respectively. The sensitivity, specificity, positive predictive value(PPV), and negative predictive value(NPV)of Lewis score were more than 70%. Conclusion CE can significantly improve the diagnostic rate of small bowel CD. Longitudinal ulcer, cobblestone appearance, and polypoid hyperplasia have higher specificity in the diagnosis of small intestinal CD. Combined with Lewis score, CD and non-CD can be more comprehensively differentiated.