Background SARS-COV-2 has caused digestive system symptom, whereas the role of which remains equivocal.Methods Patients with COVID-19 were classified into 4 groups according to symptom. The study traced the onset and duration of symptoms, compared laboratory examinations among each group and conducted bioinformatic analysis. Immune indices were further analyzed.Results By March 16, 25 patients with COVID-19 (3 with digestive system symptom, 14 with respiratory system symptom, 4 with combined symptom and 4 asymptomatic) and 13 with suspect COVID-19 were admitted to West China Hospital, Sichuan University. Digestive system symptom group had the highest level of ESR (mm/h, P༜0.0001), serum ferritin (ng/ml, P༜0.0001), hepatic enzymes (P༜0.05), and retentive lymphocyte count/percentage (P༜0.05) and its subsets (P༜0.05). Combined group (respiratory combined with subsequent digestive system symptom) had the highest level of IL-6 (pg/ml, P = 0.0046), CRP (mg/L, P = 0.0004) and moderate lymphocyte depletion while respiratory system symptom group and asymptomatic group suffered the most from lymphocyte depletion (P༜0.05). Bioinformatic analysis indicated co-expression of binding related proteins of SARS-COV-2 (ACE2, TMPRSS2 and Furin) in small intestine. CD147 was extensively expressed in alimentary tract. CTSL, PIKfyve, TPC2 and CTSB could be detected with ≥ moderate expressions in a variety of organs including alimentary system.Conclusions Alimentary system is directly attacked by SARS-COV-2 other than hyperinflammation and immune dysregulation. Involvement of alimentary system might further protect mild and moderate cases from lymphocyte depletion caused by COVID-19.