An image generation method is provided for generating an output image from an input image acquired by an image sensor that has an array of multiple pixels, each of which has arranged therein multiple sub-pixels that each receive a light beam that passes through a different pupil sub-area of an imaging optical system. The method includes a step of generating multiple parallax images that respectively correspond to the different pupil sub-areas; a step of generating multiple pixel shifted images by performing different shifting for each of the parallax images according to a virtual image forming plane of the imaging optical system; and a step of generating an output image that has a higher resolution than the resolution of the parallax images from the pixel shifted images through composition processing.