The invention relates to the technical field of coatings, and concretely discloses a water-based primer and a preparation method thereof. The water-based primer comprises a component A and a componentB; the component A comprises, by mass, an epoxy resin, an epoxy reactive diluent, a dispersant, a defoamer, a film forming aid, zinc powder, aluminum-silicon alloy powder, ferrophosphorus powder, expanded graphite, silica, a flash rust inhibitor and zirconium phosphate; the component B includes, by mass, a curing agent, and the balance of deionized water; and a mass ratio of the component A to the component B is (4-6):1. The water-based primer of the invention has the advantages of good stability, good impact resistance, good sag resistance, good drying speed, good salt spray resistance, goodflame retardant performance, simple preparation process, convenience in construction, and low production cost.