The invention discloses a water-based coating for protecting stony cultural relics, comprising a first component and a second component at a mass ratio of 1:1-1:2. The first component comprises the following ingredients in parts by mass: 5-10 parts of amino resin, 0.5-1.0 part of flatting agent, 5-10 parts of acid proofing agent and 10-15 parts of water. The second component comprises the following ingredients in parts by mass: 15-25 parts of epoxy acrylate resin, 0.5-1.0 part of dispersing agent, 0.2-0.8 part of defoamer, 5-10 parts of light stabilizer, 1-2 parts of antirust agent, 5-10 parts of abrasion-resistant agent and 20-25 parts of water. The invention also discloses a preparation method and an application method of the water-based coating for protecting the stony cultural relics. The coating disclosed in the invention can strongly bind to a stony matrix, is pollution-free, environment-friendly, colorless and transparent, and has the functions of resisting water, acid, sand impact and light aging while retaining the original appearances of stony cultural relics.