The invention relates to the technical field of coatings, and discloses a waterborne intermediate paint coating and a preparation method thereof. The waterborne intermediate paint coating is preparedfrom the component A and the component B; the component A is prepared from the following components in percentage by mass: epoxy emulsion, a dispersant, a defoamer, a coalescing agent, mica iron oxide, glass flake, fillers, barium sulfate, pigments, expanded graphite, vermiculite, silicon dioxide, an anti flash rust agent, zirconium phosphate, a base material wetting agent, a thickener and the balance of deionized water; the component B is prepared from the following components in percentage by mass: a curing agent and the balance of a coalescing agent; the mass ratio of the component A to thecomponent B is (4-8) to 1. The waterborne intermediate paint coating is good in flow resistance, stable in storage performance and anticorrosion performance, and good in adhesion, impact resistance,flame retardancy and flexibility performance.