Digital holography has applications in bio-imaging because it can simultaneously obtain the amplitude and phase information of a microscopic sample in a single shot, thus facilitating non-contact, noninvasive observation of the 3D shape of transparent objects (phase objects, which can be mapped with the phase information,) and moving objects. The combination of digital holography and microscopy is called digital holographic microscopy (DHM). In this study, we propose a compact and inexpensive smartphone-based DHM system for 3D imaging; this system includes an optical system comprising a 3D printer using commercially available image sensors and semiconductor lasers; further, an Android-based application is used to reconstruct the holograms acquired by this optical system, thus outlining the amplitude and phase information of the observed object. Also, by utilizing scalable diffraction calculation methods and touchscreen interaction, we implemented zoom functionality through pinch-in gestures. The study results showed that the DHM system successfully obtained the amplitude and phase information of the observed object via the acquired holograms in an almost real time manner. Thus, this study showed that it is possible to construct a low cost and compact DHM system that includes a 3D printer to construct the optical system and a smartphone application to reconstruct the holograms. This system is also expected to contribute to biology fieldwork and pathological diagnosis in remote areas.