The invention discloses water-in-water imitation graphite multicolor coating and a preparation method thereof and relates to the technical field of coatings. The water-in-water imitation graphite multicolor coating comprises a basic color paint, a continuous phase and protective glue; the basic color paint is made from a dispersant, a defoaming agent, talcum powder, a bactericidal agent, propyleneglycol, a pH regulator, sodium alginate, hydroxypropyl methyl cellulose, vitrified micro bubbles, heavy calcium carbonate, organic bentonite, PAE-206 multifunctional aid, a pigment, ethylene glycol methyl butyl ether, silicone acrylic emulsion, and deionized water; the continuous phase is made from a defoaming agent, a bactericidal agent, hydroxypropyl methyl cellulose, sodium alginate, PAE-206 multifunctional aid, ethylene glycol methyl butyl ether, silicone acrylic emulsion and deionized water; the protective glue is made from protective glue powder and deionized water. The water-in-water imitation graphite multicolor coating prepared herein has good water resistance, weatherability, attaching power and toughness, excellent resistance to high temperature and scour resistance, good storage stability, and good graphite imitation.