The invention provides a preparation method of an organosilicon modified polyester plasticizer. The preparation method comprises the steps of adopting organosilicone, binary acid and dihydric alcoholas raw materials, carrying out three-step-method reaction, using octamethyl siloxane and water for synthesizing under the action of a catalyst so as to obtain dihydroxy silicone oil with low molecularweight, then using the binary acid and the dihydric alcohol for carrying out esterification reaction, carrying out reduced pressure distillation to obtain a polyester, and finally reacting the dihydroxy silicone oil and the polyester under the action of the catalyst under a nitrogen condition so as to obtain the organosilicon modified polyester plasticizer. The product is non-toxic, environmental-friendly, migration-resistant, excellent in plasticity, and favorable in application prospect. The preparation method is simple in steps, convenient to operate and high in practicability.