The invention discloses a pharmaceutical composition for treating chronic gastroenteritis, which is prepared from the following raw materials: belladonna and aluminium dispersible tablets, levocarnitine, bismuth potassium citrate, metronidazole, ranitidine hydrochloride, vitamin B, lovastatin, niacin, calcium pantothenate, niacinamide, L-arginine, jujube polysaccharide, cassia seed, fructus crataegi, radix et rhizoma salviae miltiorrhizae, radix et rhizoma rhei, ginger, tartary buckwheat, radix puerariae lobatae, leucocyanidin, vitexin, astragalin, cryptoxanthin and quercetin. The pharmaceutical composition for treating chronic gastroenteritis has the synergistic effects through the compounding of the raw materials, has obvious anti-inflammatory activity, and has the advantages of both symptoms and roots treatment of the disease, obvious curative effects, convenient taking, no recurrence and no rebound after cure, little toxic and side effects, no complication, long-term use, less residues and low price, so that the production cost is reduced and the waste of resources is avoided.