The invention provides a gravel foundation bed silt removing system and a silt removing construction method. Silt in furrows and on ridge top surfaces of a gravel foundation bed can be quickly removed all around on the premise that the gravel foundation bed is not destroyed. The gravel foundation bed silt removing system comprises a mother ship, a silt removing device and a hoisting device, wherein the silt removing device is connected to the mother ship by virtue of the hoisting device; the silt removing device comprises a support frame which can be supported on the bed surface of the gravel foundation bed, and the support frame surrounds part of the bed surface of the gravel foundation bed; the silt removing device further comprises a trolley across the support frame, a disturbance assembly which is used for disturbing silt, a silt scouring assembly which is used for scouring the bed surface of the gravel foundation bed and a sucker which is used for sucking silt are connected to the trolley, and the disturbance assembly, the silt scouring assembly and the sucker can be driven by the trolley to move in the support frame; and the sucker, the silt scouring assembly and the disturbance assembly are arranged in sequence in the moving direction of the trolley.