The invention discloses a hybridization structured polysiloxane flame retardant and a preparation method thereof. The hybridization structured polysiloxane flame retardant is prepared by enabling hydrogen-containing silicone oil, allyl glycidyl ether, vinyl silane substances, phosphorus-containing active substances and a silane coupling agent to react with one another under the action of a catalyst. The flame retardant comprises a great amount of organic groups such as benzene rings, a relatively long -Si-O-Si-main chain and a hybridization structure, has hydrophobicity, is relatively high in thermal stability, comprises a great number of elements such as carbon, nitrogen, phosphorus and silicon, can be used as a carbon source and a gas source in an intumescent system, meanwhile has a synergistic flame retardant effect of multiple flame-retardant elements, is good in carbonization property and high in flame-retardant efficiency, the contact angle of the composition is up to 95 DEG C, the compatibility of the composition and a high polymer can be improved, and processing requirements of the high polymer can be met.