The invention discloses a preparation method of microwave in-situ polymerization modified short fibers. The preparation method comprises the steps of: atomizing and uniformly spraying emulsified functional polymerization monomer, initiating agent and the like on the surfaces of short fibers by utilizing an in-situ polymerization technology; carrying out a microwave radiation treatment to change the surfaces of the short fibers from smooth to rough; and carrying out grafted copolymerization reaction of the functional polymerization monomer on the surfaces of the short fibers so as to form a soft combination layer on the surfaces of the short fibers and obtain pre-treated flexible short fibers, that is, microwave in-situ polymerization modified short fibers. The microwave in-situ polymerization modified fibers prepared by the preparation method can be well dispersed and stuck in a rubber matrix; and the preparation process of the microwave in-situ polymerization modified short fibers is free from toxicity and pollution, efficient and fast, has a low usage of a modifying agent and low cost, and is easy to popularize.