The invention provides an environment-friendly waterproof antibacterial coating and a preparation method thereof. The coating is prepared from the components of organosilicon-modified epoxy resin, bisphenol-A epoxy resin, ethyl acetate, polyvinyl alcohol, bentonite, sodium dodecyl benzene sulfonate, nanometer titania, methylisothiazolinone, sodium citrate, tributyl citrate, antibacterial agent, deforming agent, dispersing agent, coalescing agent, thickening agent, isopropyl alcohol and deionized water. In the coating, the organosilicon-modified epoxy resin is matched with the bisphenol-A epoxy resin, so that the coating has high glossiness, high anti-static electricity capacity, high mechanical property, high aging resistance and high chemical corrosion resistance; the methylisothiazolinone and the antibacterial agent are added, so that the antibacterial capability of the coating can be improved effectively; moreover, the environment-friendly waterproof antibacterial coating has the advantages of low cost, environmental friendliness, high adhesive force, high extensibility, high temperature resistance and long service life; a roller coating way is adopted instead of spraying during coating, so that the production environment is improved effectively, and the physical health of workers is facilitated.