The invention discloses a full-automatic shipborne algae removal method and equipment thereof. The method comprises the following steps: 1) algae-laden water is concentrated to diluted algae pulp; 2) the diluted algae pulp is concentrated to concentrated algae pulp; 3) the concentrated algae pulp is dehydrated to form semi-solid algae puree; and 4) by water backwashing and gas backwashing methods, clear water enters a lake. A discharge hole of a rotary drum microfiltration algae removal machine is connected to a feed inlet of a first-stage concentrator through a pipeline; a discharge hole of the first-stage concentrator is connected to a feed inlet of a second-stage concentrator through a pipeline; filtered water of the two concentrators is connected to the rotary drum microfiltration algae removal machine through a return pipe; a water backwashing system is connected to a water backwashing pipe through a water pipe; a gas backwashing system is connected to gas backwashing pipes of the first-stage and second-stage concentrators through air pipes; and a power and automatic electrical control system is connected to a drive motor through a cable. The method is feasible, has advantages of no addition of a flocculant, good algae-water separation effect and good practicality, and is suitable for collection and removal of various concentrations of blue-green algae in water bodies such as lakes, reservoirs and the like.