The diagnosis of cyst structures that can be seen in almost every part of the body can be made using various medical imaging methods recently. Although the used methods and devices provide convenience in diagnosis and treatment, sometimes they can not detect early-stage cyst structures without showing any symptoms. In this study, the cystic structures with different size and formation in phantoms which are soft tissue-mimicking structures created without the need for any living tissue obtained with biopsy process are visualized by the proposed Phase Shifted-Lateral Shearing Digital Holographic Microscopy in three dimensional. The proposed method is verified with experimental results obtained by using various phantom models created at different times and structures. Experimental results illustrate the applicability of the proposed method for imaging of the cyst structures in the created soft tissue-mimicking phantoms even if they are in different structures, formations and stages (especially in early stage). In other respects, it enables to image the biological specimens in small size using simple and low-cost setup.