The invention provides a graphene modified highly-weathering-resistant and highly-rebound nanometer polymer seam filling material and a preparation method thereof, wherein the seam filling material comprises a main agent component A and an auxiliary agent component B, a mass ratio of the component A and to the component B is 1:1, the component A is prepared from the following raw materials by weight: isophorone diisocyanate, 4,4-dicyclohexylmethane diisocyanate, 2,2,4-trimethylhexamethylene diisocyanate, polyether polyol and hydrophobic nano-fumed silica, and the component B is prepared from the following raw materials by weight: a plasticizer, an antioxidant, an ultraviolet absorber, a chain extender, polyether polyol, polycaprolactone polyol, polyether ester diol, a nanometer filler, anactive nanometer graphene slurry, talc powder, organic bentonite, calcium oxide, a rheological aid, and a catalyst. The graphene modified highly-weathering-resistant and highly-rebound nanometer polymer seam filling material of the present invention has advantages of strong weather resistance and long service life, and can be exposed to the outdoor for a long time.