A micromanipulation system for applying a micro manipulation to an object within the view of a microscope, using a fine needle, comprising: a manipulator driving unit for transferring the fine needle at least along the optic axis direction of the microscope, a micro manipulation starting position determining unit for determining a micro manipulation starting position as a reference position, an object transfer unit for relatively transferring the respective positions of the object and object lens, a focus position detecting unit for detecting a focus position indicating the focus of the object in the object lens, in accordance with the relative transfer of the object, an object transfer control unit for controlling a movement of the object transfer unit, based on the detection result, and a micro manipulation control unit for performing the micro manipulation.