The imaging element of the imaging apparatus is provided with pixels respectively having multiple photoelectric conversion units that generate image signals by photoelectrically converting light fluxes that transit different regions dividing an exit pupil of an imaging optical system to a single micro lens. The imaging apparatus generates left-eye image data and right-eye image data for three-dimensional display based on image signals output by the imaging element, and generates combined image data for two-dimensional display by additively combining the left-eye image data and the right-eye image data. The imaging apparatus compresses the combined image data at a first compression rate, compresses 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 records the respectively compressed image data in the same image file.