The invention discloses an elastic aromatic polyurethane intermediate paint for railway ballast track bridge concrete bridge decks, and a preparation method thereof. The intermediate paint is prepared by mixing a component A with a component B according to a mass ratio of 5:(2-3); the A component comprises, by weight, 30-45 parts of highly-active ethylene oxide and propylene oxide copolyether ether triol, 10-15 parts of 4,4'-methylene bis(2-chloroaniline), 10-30 parts of hydroxy acrylic resin, 10-20 parts of butyl acetate, 15-22 parts of a pigment, 0.5-2 parts of an anti-settling agent, 0.5-1 part of a wetting dispersant, 0.5-1 part of an antifoaming agent and 10-20 parts of ultrafine barium sulfate powder; and the component B comprises, by weight, 40-50 parts of liquefied diphenylmethane diisocyanate, 50-60 parts of polypropylene oxide ether diol and 5-10 parts of a hexamethylene diisocyanate trimer. The elastic aromatic polyurethane intermediate paint has the advantages of high strength, good extensibility, appropriate gelling time and moderate operation time.