Provided are an apparatus and method for aligning color channels on the basis of depth information on an image taken by an imaging device equipped with a multiple color-filter aperture (MCA). An image divider generates a binary image including edge information on an original image, and generates 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 estimates color shifting vectors (CSVs) indicating shift directions and distances of color channels of the original image according to the respective ROIs. A channel matching unit obtains 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 generates a multi-focus image by combining the matched images.