A machine tool control system according to the present invention includes: a three-dimensional coordinate computing unit which calculates three-dimensional coordinates of a workpiece based on a plurality of images of the workpiece, the images being taken by the imaging apparatus from a plurality of different directions, and which calculates, from the three-dimensional coordinates, three-dimensional coordinates of a specified machining start point on the workpiece; and a coordinate converting unit which converts three-dimensional coordinates that includes the machining start point on the workpiece calculated by the three-dimensional coordinate computing unit into coordinates in the machine coordinate system for the machine tool, and which sets the converted three-dimensional coordinates of the machining start point on the workpiece, as a workpiece origin, into the machining program for the machine tool.