A control system of a machine tool which machines a work includes: a numerical control device which controls the drive axis of the machine tool based on control data; a machined surface measurement device which measures the machined surface of the work; and a data processing device, and the data processing device includes a drive axis control data acquisition portion which acquires, from the numerical control device, the chronological control data when the work is machined; a machined surface measurement data acquisition portion which acquires spatial machined surface measurement data after the machining of the work measured by the machined surface measurement device; and a data-associating processing portion which associates the chronological control data acquired by the drive axis control data acquisition portion and the spatial machined surface measurement data acquired by the machined surface measurement data acquisition portion with each other.