This new automatic bio-manipulation factory system for manipulating a single cell comprises: a bio-MEMS that transports, separates, and extracts a single cell for manipulation from a plurality of cells, controls the rotation-orientation of the extracted cell automatically, and enables the extracted cell to maintain a certain temperature; and a micro manipulation system that obtains vision information and manipulation information about the extracted single cell and the manipulation tool, provides such information to operator, manipulates the extracted single cell by transmitting the rotation-orientation feedback information and the cell manipulation order of the operator to the bio-MEMS, and manipulates the manipulation tool by transmitting the tool manipulation order of the operator to the manipulation tool. The conventional manual and individualized single cell manipulation can be automated and processed collectively by systematically combining the bio-MEMS with the micro manipulation system.