The invention relates to the technical field of blue-green algae cleaning equipment, in particular to a separation type blue-green algae collecting device and a using method. The separation type blue-green algae collecting device comprises a ship body and two floating boxes and further comprises a conveying assembly, a separation assembly, a first compacting assembly, a containing box, two collecting assemblies and two second compacting assemblies, wherein the two collecting assemblies are symmetrically arranged at the head end of the ship body, the conveying assembly is installed at the top of the ship body and located between the two collecting assemblies, the containing box is arranged at the tail end of the ship body, a filter screen is arranged in the containing box, the separation assembly is installed at the top of the ship body, the first compacting assembly is arranged between the separation assembly and the containing box, the two second compacting assemblies are symmetrically arranged at the top of the two floating boxes, and one ends of the two second compacting assemblies extend into the containing box. The blue-green algae collecting time is shortened, the collecting efficiency is improved, meanwhile, algae water is thoroughly separated from blue-green algae, the weight of the blue-green algae is reduced, and then the load of the ship body is reduced.