The invention provides water-based inner printing ink coated with PE and PP and a preparation method thereof. The water-based inner printing ink coated with the PE and the PP contains, by weight, 25-30 parts of varnish, 65-75 parts of water-based color paste and 0.1-0.3 part of defoaming agent, wherein the varnish contains, by weight, 50-70 parts of styrene-acrylate non-film-forming emulsion, 20-35 parts of acrylic resin solution or styrene-maleic anhydride resin solution, 1-3 parts of wax emulsion, 3-8 parts of coalescing agent, 0.1-0.5 part of organic amine, 0.5-1 part of wetting agent, 0.1-0.3 part of defoaming agent and 0.05-0.15 part of preservative, and the Tg value of the styrene-acrylate non-film-forming emulsion is greater than or equal to 85 DEG C. The water-based color paste contains, by weight, 20-25 parts of acrylic resin solution, 1-2 parts of wetting dispersant agent, 25-35 parts of deionized water, 40-45 parts of pigment, 0.1-0.3 part of defoaming agent and 0.05-0.15 part of preservative. The water-based inner printing ink is resistant to high temperature and abrasion, is small in chromatic aberration after being coated with PE and PP films, is high in peel strength on a basic material and can well meet the requirement of a spraying process.