The invention relates to the technical field of coatings, and particularly discloses a water-based intermediate paint and a preparation method thereof, the water-based intermediate paint comprises a component A and a component B; wherein the component A is prepared from the following components in percentage by mass: waterborne hydroxyl acrylic emulsion, nano aluminum oxide, talcum powder, bariumsulfate, titanium dioxide, graphene oxide, lithium magnesium silicate, a PH regulator, a defoaming agent, a coalescing agent, a dispersing agent, a base material wetting agent, a thickening agent andthe balance of deionized water; the component B is prepared from the following components in percentage by mass: hydrophilic modified aliphatic polyisocyanate and the balance of a cosolvent; and the mass ratio of the component A to the component B is (4-6): 1. The water-based intermediate paint disclosed by the invention has the excellent characteristics of polishing resistance, impact resistance,strong flexibility, strong adhesive force, good stability and good sagging resistance, and is suitable for outdoor high-strength operation and long-time exposed intermediate paint for vehicles.