An image pickup apparatus includes an optical system and at least one processor executing instructions to: control the optical system to pick up images while changing a focus position; combine; and detect feature points of the images picked up by the optical system and use the feature points of two images to calculate a conversion coefficient for positioning. In the controlling, in a case where the focus positions of the two images are adjacent to each other and the conversion coefficient of the two images does not satisfy a predetermined condition, image pickup is performed again with a method for controlling change of the optical system, and in the combining, two images in which the conversion coefficient satisfies the predetermined condition and focus positions of which are adjacent to each other among the images picked up by the optical system are combined.