1. An imaging apparatus comprising: an imaging element provided with pixels which respectively have multiple photoelectric conversion units that generate image signals by photoelectrically converting light fluxes that transit different regions of exit pupil of an imaging optical system to one micro lens; an image generation unit configured to generate left-eye image data and right-eye image data for three-dimensional display based on image signals output by the imaging element, and generate combined image data for two-dimensional display by additively combining the generated left-eye image data and right-eye image data; an image compression unit configured to compress the combined image data at a predetermined first compression rate, and compress the left-eye image data and the right-eye image data at a second compression rate that is higher than the first compression rate; and an image recording unit configured to record the compressed combined image data, left-eye image data, and right-eye image data in the same image file.