The invention discloses a river sediment pollution in-situ advanced treatment device and a use method thereof, the river sediment pollution in-situ advanced treatment device comprises a ship body and a box body used for treating sludge, the surface of the ship body is connected with the top of the box body through a mechanical grabbing arm, and the invention relates to the technical field of river sediment in-situ treatment. According to the in-situ deep treatment device for river sediment pollution and the use method thereof, a deep treatment method of aeration and microbial degradation, namely physical and biological treatment, is adopted, so that the river sediment pollution can be quickly degraded, the water quality of a water body is not influenced, meanwhile, certain dissolved oxygen is provided for the water body, the increase of the number and diversity of microorganisms is promoted, and secondary pollution is avoided; the device can be moved at any time for bottom mud pollution treatment, is particularly suitable for repairing bottom mud of a river containing a monitoring section, prolongs the bacterial liquid degradation time by arranging the S-shaped channel and the return pipe, and is semi-closed, so that the bacterial liquid cannot be quickly lost due to the flow velocity of a water body, the bacterial liquid degradation efficiency is enhanced, and the device is simple to operate, environment-friendly and energy-saving.