The effect of a surface cleaning using oxygen Penning discharge on the photodesorption by synchrotron radiation was measured for specially extruded 99.99% aluminum chambers. Oxygen plasma produced through a high current Penning discharge removes surface contamination without giving any damage on a surface of a vacuum chamber. This is quite a different point from a usual glow discharge cleaning. The oxygen discharge cleaning reduced the photodesorption yield of all the main components such as H-2, CO, and CO2. The total photodesorption yield for a cleaned sample was 1/10 that of an uncleaned sample at an early stage of irradiation (10(19) photons m-1). The desorption of CO and CO2 still found for cleaned samples is due to carbon contained in the oxide layer of aluminum. For further reduction of the desorption coefficient, the surface oxide layer must be removed.