1. A method of operation of a depth estimation system comprising: calculating focus measures for representing edges in a two-dimensional image for depicting a center object; generating a depth map with a control unit for the two-dimensional image based on fitting the focus measures through a Gaussian function, the depth map including an object center location corresponding to a position within the two-dimensional image for estimating a location of the center object closest to an original capturing device; and generating a three-dimensional image based on the depth map and the object center location from the two-dimensional image.