The invention relates to a special clinical nutrient composition for an inflammatory bowel disease. The special clinical nutrient composition comprises protein, amino acid, peptides, fat, carbohydrate, dietary fibers, macro-elements, micro-elements, vitamins, dietary essence, medicinal and edible components, natural plant compounds and new resource food, wherein the dietary essence comprises millet powder, oat powder and apple powder, and the medicinal and edible components comprise lanceleaf lily bulbs, wild mint herbs, ural licorice roots, Indian bread, palmleaf raspberry fruits, barbary wolfberry fruits, king solomonseal rhizome and Chinese dates. A preparation method of the special clinical nutrient composition includes the steps: preparing the components into powder in advance and uniformly mixing the powder to prepare corresponding forms; performing water extracting concentration and freeze drying on the medicinal and edible components to prepare powder, microencapsulating the vitamins and the fat into powder and freeze-drying the dietary essence into powder. Compared with the prior art, the nutrient composition can provide needed energy, key nutrients and necessary micro-elements for a patient suffering from the inflammatory bowel disease, and improve blood sedimentation, C reactive protein and intestinal mucosa permeability symptoms of the patient.