The invention discloses a water-based metal cleaner and a preparation method thereof. The water-based metal cleaner is prepared from sodium dodecylbenzene sulfonate, fatty alcohol-polyoxyethylene ether, alkylphenol polyoxyethylene, triethanolamine oleate, triethanolamine, 3-methyl-3-methoxy-1-butanol, polyphosphate, silicate, glycerol, primary sodium alkyl sulfate, isooctyl phosphate, benzotriazole, polyethylene glycol, dimethylaminoethyl methacrylate, 2-hydroyl-3-sulfopropyl starch ether and deionized water; the preparation method of the water-based metal cleaner comprises the following steps: firstly, adding a surfactant and the triethanolamine oleate to the glycerol, heating and stirring, next, adding the triethanolamine, the 3-methyl-3-methoxy-1-butanol, the polyphosphate and the silicate, adding the primary sodium alkyl sulfate, the isooctyl phosphate, the benzotriazole and the polyethylene glycol under the conditions of stirring and preserving heating, and finally adding the rest components under the conditions of stirring and preserving heating, and heating and stirring to obtain the cleaner. The water-based metal cleaner has excellent cleaning performance and relatively high corrosion inhibition period.