The invention discloses a cleaning fluid for removing rust, a preparation method and application thereof, and belongs to the technical field of chemical rust removal. The cleaning fluid comprises 2%-10% of an organic acid, 0.5%-4.5% of an organic acid salt, 10%-25% of a chelating agent, 2%-6% of a permeation aiding solvent, 0.15%-0.25% of a corrosion inhibitor and the balance of water, wherein theorganic acid is 2-hydroxy propane-1,2,3-tricarboxylic acid and/or 2,3-dihydroxy succinic acid, the organic acid salt is 8-hydroxyquinoline citrate or 2,3-sodium tartrate, and the chelating agent is tetrasodium glutamate diacetate. The cleaning fluid is high in scale dissolving rate, high in descaling rate, low in corrosion rate, good in biodegradability is good and particularly suitable for removing the rust in the oil field.