The invention discloses a water jet hull rust remover and an operating method thereof. The rust remover comprises a high-pressure water tube interface, a high-pressure water tube interface seat, a rust removing disk, a high-pressure water tube interface seat support, a nozzle, and a nozzle rotary frame, and also comprises an air tube interface, an air tube interface seat, an air motor body, a vacuum recycling flange, a vacuum recycling tube, a vacuum recycling opening, and a high-pressure water sealing ring, wherein the vacuum recycling opening is embedded in the rust removing disk and connected with the vacuum recycling tube; the outlet end of the vacuum recycling tube is connected with the vacuum recycling flange; and the upper surface of the rust removing disk is also provided with a height adjusting support. The method comprises steps of height adjustment, rust removal and recycling. In the water jet hull rust remover, the rust removal by the superhigh pressure water jet and pumping and slag discharging by the vacuum system are compatibly designed into one body, the vacuum equipment recycles the rust, the high temperature, which is over 80 DEG C and generated by the water jet action, in the vacuum cavity can cause certain positive effects on the evaporation of water of the bulkhead, the rust removal drying is realized, and the hull is avoided from the return of rust.