The invention discloses a metal bearing water-based cleaning agent and a preparation method and application thereof. The cleaning agent comprises the following components in percentage by mass: 2 to 8 percent of fatty alcohol polyoxyethylene ether, 2 to 8 percent of alkylphenol polyoxyethylene ether, 3 to 10 percent of fatty acid alkanolamide, 5 to 25 percent of triethanolamine oleate, 10 to 22 percent of triethanolamine, 5 to 18 percent of monoethanolamine, 0.5 to 3 percent of alkyl sodium sulfonate, 0.01 to 0.5 percent of benzotriazole, 1 to 2 percent of disodium ethylene diaminetetraacetate and 3.5 to 71.49 percent of water. During use, the cleaning agent is prepared into 2 to 10 percent working solution, and a bearing part is ultrasonically cleaned, rinsed, subjected to spray washing and dried to meet the cleaning degree standard and the finished product vibration value standard. The product is environment-friendly, does not influence a bearing material, is prepared from readily available raw materials, has low cost, can replace the conventional cleaning gasoline and kerosene, reduces the potential safety hazard, avoids environmental pollution, and saves energy.