The invention discloses a scale remover for a water injection well, and a preparation method and an application of the scale remover, and belongs to the field of oil field development. The scale remover comprises the following components, by mass, 25-40% of a scale-dissolving agent, 3-6% of a dispersant, 3-6% of a corrosion inhibitor, 3-6% of a cleanup additive, and 1-3% of a suspending agent, with the balance being water. The scale-dissolving agent is a hydrochloric acid solution having a concentration of 25-37%; the dispersant is selected from at least one of carboxymethyl cellulose, sodium dodecyl sulfate, and 1-methylpentanol; the corrosion inhibitor is chloridized benzylquinoline quaternary ammonium salt; the cleanup additive is selected from at least one of dodecylpyridinium bromide, hexadecylpyridinium bromide, and octadecylpyridinium bromide; and the suspending agent is lignin. The scale remover can deeply remove scale, has a corrosion inhibition function, is easy to flow back, and doesn't cause secondary pollution on the stratum.