Our objective was to analyse the clinical characteristics of systemic lupus erythematosus (SLE) patients with gastrointestinal manifestations. Medical charts of 177 hospitalized SLE patients were systematically reviewed, including demographic data, clinical features, laboratory findings, and treatments, as well as outcomes. Thirty-nine cases (22.0%) had SLE-related gastrointestinal manifestations, and in 12 cases (30.8%), gastrointestinal manifestations occurred as the initial symptoms. Twenty-five cases (64.1%) had abdominal pain, 22 cases (56.4%) had nausea and vomiting, 12 cases (30.8%) had diarrhea, and gastrointestinal hemorrhage occurred in three cases (7.7%). Protein losing enteropathy and intestinal pseudo-obstruction were the most common identifiable gastrointestinal complications, though other reasons such as superior mesenteric venous thrombosis, pancreatitis, peritonitis, and liver impairment could also occur in SLE. The incidences of Raynaud's phenomenon and pyeloureterectasis were significantly higher in patients with gastrointestinal complications than those without (p < 0.05). Multivariable analysis indicated Raynaud's phenomenon, decreased C3, CH50, and anti-neutrophil cytoplasmic antibody positivity were independent predictors of gastrointestinal involvements (p < 0.05). Gastrointestinal complications are common, diverse, and could be the initial and major manifestations of lupus. SLE patients who had Raynaud's phenomenon, hypocomplementemia and positive anti-neutrophil cytoplasmic antibody were at increasing risk of developing gastrointestinal complication.