The invention relates to a plugging remover for a water injection well containing accumulated sewage, a preparation method and an application thereof. The plugging remover contains the following components by weight percent: 15.0-30.0% of peracetic acid, 1.0%-3.0% of hydrofluoric acid, 1.0%-2.0% of corrosion inhibitor, 0.5%-1.0% of surface active agent and the balance of water. The invention also provides a preparation method for the plugging remover and the application thereof. The plugging remover provided by the invention can solve the problems that the plugging of the water injection well containing accumulated sewage is serious and a common plugging remover cannot effectively remove organic and inorganic compound plugging. The plugging remover provided by the invention is capable of removing the plugging, has less corrosion to the well shaft and equipment, can guarantee normal production and injection, can increase the yield and the economic benefit, can reduce the maintenance and treatment cost, has obvious social benefit and has wide application prospect.