The invention discloses an environment-friendly water-based metal cleaner and a preparation method thereof. The environment-friendly water-based metal cleaner is composed of the following components of, by mass, 5-30% of a nonionic surfactant without APEO, 0.1-5% of a cationic surfactant, 0.1-15% of an inorganic washing assistant, 0.3-5% of a chelating agent, 0.5-6% of a corrosion inhibitor, 0.5-7% of an anti-redeposition agent, 0.5-3% of a penetrating agent, 0.1-8% of an alcohol ether solvent, and the balance water. The preparation method of the environment-friendly water-based metal cleanercomprises the following steps that the inorganic washing assistant and the chelating agent are added in the water and evenly mixed; then the nonionic surfactant without the APEO, the cationic surfactant, the corrosion inhibitor, the anti-redeposition agent, the penetrating agent and the alcohol ether solvent are added and evenly mixed; and the environment-friendly water-based metal cleaner is obtained. The environment-friendly water-based metal cleaner is free of phosphorus, nitrite and the APEO, good in anti-rust performance, good in stability, free of stimulation, safe, environmentally friendly and simple in preparation technology.