A system for merging differently focused images includes a computer for including a merge images program which includes a read module for reading a plurality of the differently focused images of an object disposed on a platform of a measuring machine, one image thereof as a first image (BMP), another image thereof as a next image (BMP0), and reading gray values of pixels and computing a gradient of each pixel; a determining module for determining whether the gradient (G) of each pixel in the BMP is less than the gradient (G0) of a corresponding pixel in the BMP0; and a merge images module for updating/replacing the gray value (P) and the G of the pixel in the BMP with the gray value (P0) and the G0 of the corresponding pixel in the BMP0 if the G of the pixel in the BMP is less than the G0 of the corresponding pixel in the BMP0. A related method is also provided.