Recently, performances of the optical devices are improving with miniaturization their sizes such as the development of the photonic crystal. So, precise shape measurement with non-invasive evaluation technique is required to observe edge or steep surface of photonic crystal to evaluate the quality. Thus, we propose the method to obtain 3D nanostructure by using phase-shifting digital holography system. Phase-shifting digital holography is the method to obtain the complex amplitude of the sample through some phase-shifted holograms. It is considered that the holography system has the nano meter resolution in axial direction and is able to achieve the nano defect detection for the photonic crystal devices. In this paper, we suggest a novel phase-shifting digital holography method applied optical heterodyne interferometer. Optical heterodyne interferometer is the method using two different (close-by) wavelengths of light for object light and reference light, and interferential intensity distribution changes temporally with their different frequencies. We suggest a novel phase-shifting digital holography method applied optical heterodyne interferometer. Four phase-different signals can be acquired from the time-domain heterodyne signal based on cycle of beat signal.