The change of effective aperture in adaptive optics system may lead to light shortage among some of the Hartmann-shack sensor sub-apertures and functional failure in a number of actuators, making the matching layout between system sub-aperture location and actuator location changes. The correspondence between the control voltage input of actuator and the feedback output of sub-aperture, therefore, changes consequently. In response to the effective layout change of the adaptive optics system, this paper firstly discussed the influence of the change of aperture on adaptive optics system and analyzed the reasons for instability. It then put forward a new method based on 0-1 fault model to model the partial failure situation in the system so as to modify proportional-integral control algorithms. Finally, it proved that through experiments using the 0-1 fault model can guarantee the stable operation of the system, but the failure of some parts of the adaptive optics system will lead to the decrease of the correction ability of the system to the wavefront aberration.