Objective To evaluate the value of balloon-assisted enteroscopy (BAE) in the differential diagnosis of small bowel stenostic Crohn's disease (CD) and other non-infectious benign small bowel stenosis. Methods The clinical data of 67 patients with benign small bowel stenosis who were admitted to the Air Force Medical Center from Oct. 2014 to Jun. 2021 were retrospectively analyzed. The diagnosis and treatment process and outcomes after BAE of the included patients were followed up. Consistency between the clinical diagnosis based on BAE and final diagnosis was evaluated. The value of BAE in the differential diagnosis of small bowel stenostic CD and other non-infectious benign small bowel stenosis was evaluated, and the endoscopic performance in patients with small bowel stenostic CD and other non-infectious benign small bowel stenosis were compared. Results Among the 67 patients with benign small bowel stenosis, 4 were lost to follow-up, 2 were diagnosed as lymphoma after follow-up, and finally 61 were included in this study. The follow-up period was 28 (4-73) months until Oct. 30, 2021. The etiologies of benign small bowel stenosis were CD (62.3%, 38/61), cryptogenic multifocal ulcerous stenosing enteritis (CMUSE) (11.5%, 7/61), small intestinal tuberculosis (6.6%, 4/61), ischemic enteritis (4.9%, 3/61), radiation enteritis (3.3%, 2/61), non-steroidal anti-inflammatory drug-related enteritis (1.6%, 1/61), eosinophilic enteritis (1.6%,1/61), Meckel's diverticulum-related small bowel stenosis (1.6%, 1/61), intestinal Behcet's disease (1.6%, 1/61), and unclear (4.9%, 3/61). The overall consistent rate between BAE-based clinical diagnosis and final diagnosis was 80.3% (49/61). The sensitivity and specificity of BAE in the diagnosis of small bowel stenostic CD were 97.4% and 82.6%, respectively. Small bowel stenostic CD patients showed more non-transverse ulcers at the stenosis and more intestinal nonstenostic ulcers in the ileum than other non-infectious benign small bowel stenosis patients (53.1%[17/32] vs 16.7%[3/18], 38.9%[14/36] vs 0; both P<0.05). No significant differences were detected in the location, degree, morphology, or the presence of fibrotic stenosis or multiple stenosis between the 2 groups (all P>0.05). Conclusion BAE has high value in the differential diagnosis of small bowel stenostic CD and other non-infectious benign small bowel stenosis, but it still needs to be combined with clinical manifestations, other examination methods, and long-term follow-up.