Aperture synthesis is an important approach to improve the lateral resolution of digital holography (DH) techniques. The limitation of the accuracy of registration positions between sub-holograms affects the quality of the synthesized image and even causes the failure of aperture synthesis. It is a major issue in aperture synthesis of DH. Currently intensity images are utilized to find the registration positions of sub-holograms in aperture synthesis. To improve the accuracy of registration positions, we proposed a method based on similarity calculations of the phase images between sub-holograms instead of intensity images. Furthermore, a quantitative indicator, degree of image distortion, was applied to evaluate the synthetic results. Experiments are performed and the results verify that the proposed phase-image-based method is better than the state-of-the-art intensity-image-based techniques in the estimation of registration positions and provides a better synthesized final three-dimensional shape image.