Aspherical or free-form optical surface machining using an ultra-precision machine tool is a common and effective method in precision optics manufacturing. However, this method sometimes causes waviness due to the machine’s motion in mid-spatial frequency (MSF) form deviations. This waviness lowers the quality of the optical surface. To address this problem, we use the waviness of the axial displacement of the ultra-precision machine tool. The waviness is obtained by a non-contact on-machine metrology (OMM) system that measures an optical flat as a correction reference curve, which is used to correct the surface of the workpiece to reduce the effect of waviness in advance. The OMM system consists of a displacement probe and a machine tool axis position capture device. The probe system uses a confocal chromatic probe on an ultra-precision machine tool to evaluate the form deviation of the workpiece with 1 nm resolution. The axis position capture system uses a signal branch circuit of linear scale on each axis from the ultra-precision machine tool. The OMM system is tested in terms of accuracy and repeatability. In comparison to the results of the shaper cutting of an oxygen-free copper (OFC) workpiece with feed-forward correction, we were able to reduce the profile error from 125.3 nm to 42.1 nm in p-v (peak to valley) and eventually also reduced the waviness.