The invention discloses a water-based flexographic printing ink for cigarette tipping paper printing and a preparation method thereof. The water-based flexographic printing ink is composed of a modified acrylic emulsion, pigment and filler, a wetting dispersant, a transfer printing agent, a defoaming agent, deionized water, and a cosolvent. The modified acrylic emulsion is a novel acrylic emulsion formed by copolymerization of an imported high quality emulsifier, acrylate and special functional monomers, and has the advantages of fantastic calcium ion stability, dilution stability, mechanical stability and freeze-thaw stability, and small pollution to the environment. The water-based flexographic printing ink for tipping paper printing provided by the invention is non-toxic and tasteless, has quick drying speed and good dispersion stability, the printing product is free of deformation and edge curling, and has bright color and excellent antibacterial properties. The printing product has few residual monomer and low odor, is green and environment-friendly, the printing ink can be used cooperatively with a flexographic press, the printing speed can reach 250-300m / min, and the machine speed is doubled than the traditional intagliotipping paper printing press, thus greatly improving the production efficiency, and saving the production cost.