The invention provides a neutral rust-proof water-based cleaning agent. A raw material of the agent contains a phosphorus-free cleaning auxiliary agent, a metal corrosion inhibitor, a surfactant, a solubilizer, a defoaming agent and water. The invention further provides a preparation method of the neutral rust-proof water-based cleaning agent. According to the neutral rust-proof water-based cleaning agent, foam is low, a plurality of cleaning modes such as spray cleaning, ultrasonic cleaning and bubbling cleaning can be adopted, the application range is wide, the use method is flexible and diversified, the good cleaning effects on grinding oil, cutting fluid, metal powder and the like in the production and processing processes of various metal devices are realized, no influence is generated on subsequent surface treatment, and a certain rust-proof function is achieved; and the cleaning agent is easy to biodegrade and process and discharge, the compatibility with different metals is better, the cleaning and rust-proof performance are very high, the preparation process is simple, the preparation difficulty is reduced, and the manpower requirement is reduced.