Digital holography has transformative potential in measuring stacked-chip microstructures due to its noninvasive, single-shot, full-field characteristics. However, uncertainties in reconstruction distance inevitably lead to resolving blur and reconstruction distortion. Herein, we propose a phase-based reconstruction optimization method that consists of a phase-evaluation function and a structured surface-characterization model. Our proposed method involves setting a reconstruction distance range, obtaining phase information using sliced numerical reconstruction, and optimizing the reconstruction distance by finding the extreme value of the function, which identifies the focal plane of the reconstructed image. The structure of the surface topography is then characterized using the characterization model. We perform simulations of the recording, reconstruction, and characterization to verify the effectiveness of the proposed method. To further demonstrate the approach, a simple holographic recording system is constructed to measure a standard resolution target, and the measurement results are compared with a commercial instrument. The simulation and experiment demonstrate, respectively, 31.16% and 34.41% improvement in step-height characterization accuracy.