A numerical controller which gives an instruction to a machine tool that uses a main shaft motor (5) to return to the origin, in order to control the position of a tool. The main shaft can be returned to the origin by simply giving an instruction for returning to origin to a main shaft amplifier (SPA) that drives the main shaft motor (5). Prior to CNC-operating the machine tool according to the invention, the grid shifting amount (P2) determined by a relationship of the main shaft motor (5) and the object to be controlled is set to the side of the spindle amplifier (SPA), and position data (P3) corresponding to a distance from the origin of machine to a machining starting point transferred prior to a predetermined position stop instruction and the grid shifting amount (P2) are added up together. Therefore, when the instruction for returning to origin is produced from the numerical controller to the spindle amplifier, the position control is automatically assumed, and the moving operation is started with respect to a desired position.