The invention discloses an organic silicon graft modification polyester type polyurethane prepolymer and preparation and application thereof. The preparation method comprises the following steps of: stirring 10-75 parts by weight of diisocyanate, 3-25 parts by weight of single-terminal hydroxy polysiloxane and 0.1-0.5 part by weight of organic metal catalyst at 90-100 DEG C for reaction, then adding 100 parts by weight of polyester polyol, and stirring at 60-90 DEG C for reaction to prepare the organic silicon graft modification polyester type polyurethane prepolymer. According to the invention, a prepolymer subjected to graft modification can be mixed with the polyurethane prepolymer synthesized from the diisocyanate or polyisocyanate and the polyester polyol in a mutually matching way, and a polyurethane elastomer can be prepared by adding a chain extender; the prepared polyurethane elastomer is greatly improved in surface property and obviously enhanced in water resistance and heat resistance. The preparation method disclosed by the invention has the advantages of low cost and easiness for obtaining of raw materials, simple synthetic step, moderation in reaction speed, easiness for control of operational conditions and suitability for industrialized production without environment pollution and accords with the development direction of a green material.