1. An apparatus for aligning color channels, comprising: an image divider configured to generate a binary image including edge information on an original image taken by an imaging device having different color filters respectively installed in a plurality of openings formed in an aperture, label respective components including pixels connected with each other in the binary image, and thereby generate a label map including a plurality of regions of interest (ROIs) respectively corresponding to a plurality of objects included in the original image; a shifting vector estimator configured to estimate color shifting vectors (CSVs) indicating shift directions and distances of color channels of the original image according to the respective ROIs on the basis of frequency components of image data constituting the respective ROIs; and a channel matching unit configured to obtain a plurality of matched images corresponding to the respective ROIs included in the label map by shifting the color channels according to the respective CSVs, and generate a multi-focus image focusing on all the plurality of objects included in the original image by combining the matched images.