We report here on the application of a digital holographic microscope as a metrology tool for the inspection and the micro-topography reconstruction of different micro-structures of phase shift photo-mask (PSM). The lithography by phase shift photo-mask uses the interference and the pattern of the PSM is not imaged by general optical microscope. The technique allows us to obtain digitally a high-fidelity surface topography description of the phase shift photo-mask with only one hologram image acquisition, allowing us to have relatively simple and compact set-ups able to give quantitative information of PSM.