The invention provides novel water in water multicolor paint and the preparation method, which belongs to the technical field of paint preparation. Dispersant, pigment, calcium carbonate, film forming additive, antifoaming agent, thickening agent, ammonia water and anti-corrosion agent are added into the dispersing pot, after being uniformly mixed and grinded, synthetic resin emulsion and antifoaming agent are added and mixed, then thickening agent is added, thus water dispersing phase is manufactured; water, dispersant, antifoaming agent, cellulose and anti-corrosion agent are added in a container, after being mixed uniformly, water soluble resin is added and mixed, thus protective glue is manufactured; organobentonite is added in warm water and mixed to colloid, aluminum sulfate and magnesium chloride is added and mixed, thus water dispersing medium is manufactured; the water dispersing medium is added into a blender, and the water dispersing phase and the protective glue are being added while being mixed, after being cut and stirred by a screen, the water in water multicolor paint with various colors mixed and surface of dispersed particle colloidized is obtained, the paint dispersing medium and the dispersing medium is apparently separated, the gloss is high, and the decorative effect and the stability are good.