1. An image acquisition apparatus, comprising: a pixel shifting unit moving a relative position between a luminous flux entering an image pickup device and the image pickup device to a plurality of predetermined positions in a predetermined order; a shooting unit shooting an image of a subject image formed by the luminous flux on a photoreception surface of the image pickup device when the relative position is placed in any of the plurality of predetermined positions; a high-resolution image generation unit combining a plurality of images obtained by shooting the images by the shooting unit and generating a high-resolution image of the subject having higher resolution than the images; a prediction unit predicting a shooting environment when the shooting unit afterwards shoots the images of the subject on a basis of a change of at least two images obtained by shooting the images by the shooting unit; and a shooting condition setting control unit controlling a setting of a shooting condition when the shooting unit shoots an image of the subject image on a basis of a result of predicting the shooting environment by the prediction unit.