BACKGROUND: COVID-19 can affect multiple organ systems beyond the respiratory tract, including the gastrointestinal tract, where gastrointestinal symptoms include nausea, vomiting, diarrhea, abdominal pain, and even serious manifestations such as ulcers, perforation, or gastrointestinal bleeding. CASE PRESENTATION: We report a case of a 45-year-old male patient with small bowel ulcers caused by chronic COVID-19 infection. Initially presenting with fever and transient unconsciousness, he developed ischemic necrosis and required a mid-thigh amputation. Despite treatment with anti-infection therapy, extracorporeal membrane oxygenation, and continuous renal replacement therapy, he experienced persistent abdominal pain and gastrointestinal bleeding. Imaging and colonoscopy confirmed partial small bowel obstruction and inflammation. After treatment with methylprednisolone and enteral nutrition, his symptoms improved. However, he suffered a gastrointestinal perforation requiring emergency surgery and later underwent a successful stoma reversal. The patient was subsequently discharged with improvement and was discharged with a primary diagnosis of "enterostomal status, perforation of small intestinal ulcer, viral myocarditis, COVID-19 infection, and post right lower extremity amputation". During the past year of follow-up, the patient has not experienced any recurrence of abdominal pain or rectal bleeding. CONCLUSION: Although coronavirus pneumonia combined with small bowel ulcers is rare, it requires emergency treatment and has a high mortality rate. This case highlighted the severe gastrointestinal complications induced by COVID-19 infection and the effectiveness of comprehensive management strategies.