BACKGROUND: Common variable immunodeficiency (CVID) is a primary antibody immunodeficiency disorder characterized by diminished IgG levels. Despite ongoing research, the precise pathogenesis of CVID remains unclear. Genetic factors account for only 10%-20% of cases, with an estimated incidence of 1 in 10000 to 1 in 100000, affecting individuals across all age groups. CASE SUMMARY: We report the case of a 32-year-old man with CVID who presented with a chief complaint of "recurrent diarrhea and significant weight loss over the past 2 years". Laboratory tests on admission showed fat droplets in stool, while other parameters were within normal ranges. Gastroscopy revealed a smooth gastric mucosa without bile retention or signs of Helicobacter pylori infection; however, the mucosa of the descending segment of the duodenum appeared rough. Further evaluation of the small intestine using computed tomography indicated no abnormalities. Finally, the whole-small bowel double-balloon enteroscopy (DBE) was performed, which revealed various phenotypic changes in the small intestinal mucosa. The patient was diagnosed with CVID, which improved after immunoglobulin therapy, with favorable follow-up outcomes. CONCLUSION: Non-infectious enteropathy in CVID is rare. Therefore, DBE is essential for diagnosing small intestinal involvement in such cases.