This invention relates to a method of preparing amphiphilic silicon-containing cross-linking agent and its application method, wherein an isocyanic acid reaction and a capping reaction are used to prepare a hydrophilic/hydrophobic amphiphilic silicon-containing cross-linking agent with excellent biocompatibility, high strength, and high cross-linking degree. The amphiphilic silicon-containing cross-linking agent is suitable for the development in biomedical material-related fields.本發明係一種兩性含矽交鏈劑之製備方法及其應用方法,其係利用異氰酸反應和封端反應製備得一具有生物相容性良好、強度佳、交鏈程度高的親、疏水性兩性含矽交鏈劑,此兩性含矽交鏈劑十分適合發展於生醫材料之相關應用領域。