The invention discloses a cleaning ship for phytoplankton. The cleaning ship is in a double ship structure and is composed of a driving wheel, a refuse guide mechanism, an impeller water distributor, a refuse tipping mechanism, a refuse cabin, a water plant cutting and collecting mechanism, a drive control system and other parts. When the ship works, the refuse in front of the ship is sucked into a tipping bucket refuse collecting area through a refuse guide mechanism and an impeller distributor, and then the refuse collected by the refuse tipping mechanism is poured into the refuse cabin on the ship; meanwhile, the phytoplankton and macrophyte are cut by an aquatic plant cutting mechanism, and then are transported to the refuse cabin through a water plant collecting mechanism (i.e. a rake type conveying crawler), after the refuse is full of the refuse cabin, a ship body docks, and the refuse is hung to a transfer trolley through a hoist. The cleaning ship is fast in speed of clearing away the refuse and phytoplankton on the water surface, and is capable of preventing the phenomenon that a cutter is twisted by the water plants.