A Fresnel zone plate (FZP) is a micro-focusing optical element of synchrotron radiation hard X-ray. Our developed multilayer FZP produced a sub-micron size spot at the hard X-ray energy and the focusing efficiency is about 25%. However the higher efficiency FZP is required to utilize the sub-micron probe in microscopy, diffraction and imaging applications. A kinoform FZP composed of gradient refractive index phase zones has the advantage of a high focusing efficiency compared to the conventional multilayer FZP. In order to fabricate the kinoform FZP, we developed a computer-control system. The developed computer-control system automatically operates whole combinatorial deposition processes of the kinoform FZP by inputting the optical parameters of the FZP (focal length, X-ray wavelength, number of zones, zone materials).