The invention discloses a waterproof ink for packaging and printing and a preparation method thereof. The raw materials include: maleic resin, water-soluble acrylic resin, carboxymethyl cellulose, ethyl acetate, isopropanol, a stabilizer, a leveling agent, a defoamer, a dispersant, a waterproof agent, a slipping agent, pigments, xanthan gum, Arabic gum and fine pored silica gel. The specific stepsinclude: 1) mixing and heating maleic resin, water-soluble acrylic resin, carboxymethyl cellulose, ethyl acetate and isopropanol, and then performing stirring to obtain an emulsion; 2) heating the stabilizer, the leveling agent, the defoamer, the dispersant, the waterproof agent, the slipping agent and the pigments, then conducting ultrasonic vibration to obtain an auxiliary material; and 3) mixing xanthan gum, Arabic gum and fine pored silica gel, then adding the mixture into the emulsion, then adding the auxiliary material, performing high-speed stirring, and then conducting grinding. The ink prepared by the method provided by the invention has the advantages of simple process, low cost, good waterproofness, firm adhesion, etc., and has broad market prospects.