In the semiconductor industry, the integrated circuit density is getting higher, which leads to a smaller margin of error for the bonding process. Therefore, accurate adjustments before bonding are often necessary. An accurate image alignment under a vision system is usually required to fine-tune the bonding position. However, a considerable depth of focus is sacrificed for sufficient resolution of the object, limiting the optics operation range. Digital holographic microscopy with digital refocusing is applied as an enhancement to extend the depth of focus. The proposed algorithm merges the image alignment method with a refocusing algorithm to extend the image alignment capability with digital holography. Tested with simulated images, the proposed algorithm showed no significant deviation to simulated parameters. Also, the alignment result is robust among several test patterns. Moreover, the overall time is reasonable for industrial application.