The invention discloses a method for preparing sheep enoxaparin sodium from sheep intestinal mucosa heparin. The method comprises the following steps: 1, preprocessing sheep heparins; 2, preparing a sheep heparin quaternary ammonium salt; 3, preparing sheep heparin benzyl ester; and 4, carrying out alkali depolymerization on the sheep heparin benzyl ester, decoloring, neutralizing by using an acid, carrying out alcohol precipitation, refining, and drying to obtain finished sheep enoxaparin sodium. The simple and efficient method for preparing the sheep enoxaparin sodium from the sheep intestinal mucosa heparin is screened and established, and researches of the systemic physical and chemical properties, the biological activity and the molecule structure are carried out on the prepared sheep enoxaparin sodium. The sheep enoxaparin sodium prepared in the invention completely accords with USP37 and EP8.0 quality release criteria of sheep enoxaparin sodium, and has extremely high practical values and medical application prospect. The sheep enoxaparin sodium has the advantages of simple and easily available raw material, controllable quality, no existence of bovine spongiform encephalopathy virus risk, promotion of the effective utilization of sheep culture and slaughter wastes (intestinal mucosa), and great economy potential.