The invention discloses a nanosilicon dioxide modified polyurethane elastomer and a preparation method thereof. The preparation method comprises the steps of enabling polyether glycol, isocyanate and micromolecular dihydroxy alcohol to be subjected to addition polymerization reaction to prepare a polyurethane prepolymer as a component A; uniformly mixing a chain extender, ethyl silicate and a silane coupling agent, carrying out in-situ hydrolysis on ethyl silicate to form nanosilicon dioxide particles, performing surface hydrophobicity modification on the nanosilicon dioxide particles by using the silane coupling agent, and removing a solvent in the mixture to obtain a component B; uniformly mixing the component A and the component B according to a certain ratio, degassing, pouring and carrying out vulcanization molding to obtain the nano-modified polyurethane elastomer. By using the preparation method, the uniform dispersion of silicon dioxide particles in polyurethane is realized, the enhancement effect of nanoparticles is sufficiently taken, the prepared polyurethane elastomer is obtained by crosslinking the nanosilicon dioxide particles, and the heat resistance and chemical stability of the polyurethane elastomer can be remarkably improved; in addition, the nanosilicon dioxide modified polyurethane elastomer can meet the requirements of a sealing element for mechanical strength, wear resistance, high elasticity and oil resistance and has a wide market prospect.