The invention discloses water-based anti-rusting liquid. The water-based anti-rusting liquid comprises raw materials of, by weight, 15-25 parts of isopropanolamine, 3.1-5.2 parts of boric acid, 25-30 parts of dimethyl dodecanedioate, 2-5 parts of a rare earth corrosion inhibitor, 1-2 parts of sodium molybdate, 4-6 parts of tartaric acid, 0.1-0.3 part of a defoaming agent, 0.1-0.2 part of a surfactant, 0.1-0.3 part of a sterilizing agent and 42-52 parts of water. The invention further discloses a preparation method of the water-based anti-rusting liquid. The preparation method includes the following steps that the raw materials are weighed according to the weight parts, the boric acid, the isopropanolamine and xylene are evenly mixed, and backflow, reduced pressure distillation and vacuum drying are conducted to obtain a material A; the material A and the dimethyl dodecanedioate are evenly mixed, heated and stirred, and then vacuum drying is conducted to obtain a material B; and the material B, the rare earth corrosion inhibitor, the sodium molybdate, the tartaric acid, the defoaming agent, the surfactant and the sterilizing agent are evenly mixed and then stirred after water is added, so that the water-based anti-rusting liquid is obtained. The water-based anti-rusting liquid is good in anti-rusting performance and free of environment pollution.