The invention discloses a silicon-based polymer filling material for coal mines, and relates to the technical field of filling materials for the coal mines. The silicon-based polymer filling materialis prepared from a component A and a component B through mixing, wherein the mass ratio of the component A to the component B is (1.2-1.6):1, the component A is prepared from water glass, a compositecatalyst, a foam stabilizer and a surfactant through mixing, and the component B is prepared from isocyanate, a flame retardant and a plasticizer through mixing. The invention also discloses a preparation method of the silicon-based polymer filling material for the coal mines. The silicon-based polymer filling material has the advantages of environment protection, adjustability in expansion times,low heat storage and self-extinguishing, solving the problems of poor environmental protection property, low tight-filling rate, high heat release and no flame retardance of current filling materialsfor the coal mines.