An image pickup system includes an image pickup apparatus and a mount adaptor that adjusts a flange focal length between the image pickup apparatus and an interchangeable lens. The mount adaptor includes a phase-difference focus detection unit that can output a first phase-difference focus detection signal, and an optical device that separates first incident light into second and third incident light. The first incident light is transmitted from the interchangeable lens. The second incident light enters the image pickup apparatus. The third incident light enters the phase-difference focus detection unit. The image pickup apparatus includes an image pickup device that can output a second phase-difference focus detection signal, and a controller that selects either of the first phase-difference focus detection signal and the second phase-difference focus detection signal on the basis of satisfaction of a predetermined condition and performs focusing.