A method for the automatic phase-distortion compensation in digital holography is proposed, in which the image segmentation technique is used to automatically segment the detected objects, thus a phase mask is generated, and the phase-distortion in areas without containing the detected object region is further obtained. The least-squares fitting of phase-distortion based on the phase-distortion correction model is done and the automatic phase-distortion compensation is eventually achieved. In experiments, a built-in digital holographic inspection platform is established and the wafer surface measurement is conducted. The results show that the proposed method can be used to automatically correct phase-distortion.