The invention discloses biocompatible polyurethane modified by sulfonated hydroxypropyl chitosan and a method for preparing the biocompatible polyurethane. The method includes synthesizing the sulfonated hydroxypropyl chitosan from chitosan by means of etherification reaction and sulfonation treatment, then adding diphenyl-methane-diisocyanate, polyethylene glycol and catalysts into a reactor and carrying out stirring reaction under the protection of nitrogen at the temperatures of 70-80 DEG C for 2-4 h; adding the sulfonated hydroxypropyl chitosan into reaction products and carrying out cooling reaction for 6-12 h to obtain the biocompatible polyurethane modified by the sulfonated hydroxypropyl chitosan. The biocompatible polyurethane and the method have the outstanding advantages that the sulfonated hydroxypropyl chitosan which is a water-soluble heparinoid substance is covalently grafted on polyurethane long chains, and accordingly the hydrophilicity and the anticoagulation properties of polyurethane can be greatly improved; processes are simple, reaction conditions are mild and are easy to control, and raw materials are easily available and are low in cost.