The invention discloses a seal primer for railway ballast track concrete bridge decks as well as a preparation method and an application of the seal primer. The seal primer is prepared from a component A and a component B in a mass ratio being 1:0.8-1 by mixing, wherein the component A comprises raw materials in parts as follows: 20-40 parts of low-molecular-weight solid epoxy resin, 20-40 parts of butyl acetate, 5-20 parts of methyl isobutyl ketone and 20-40 parts of isopropanol; the component B comprises raw materials in parts as follows: 10-30 parts of a polyamide curing agent, 30-60 parts of xylene, 1-5 parts of normal butanol and 20-40 parts of isopropanol. The seal primer for the railway ballast track concrete bridge decks can permeate into gaps of a concrete base to seal the gaps of the concrete base, and adhesion force between an elastic polyurethane intermediate coat and the concrete base is improved.