To meet the accuracy of the high power lasers auto-alignment system, a new method of elliptic light spot differential quick adjustment in the state of non-vertical was put forward, introducing the local adaptive threshold and binarization algorithm which improve the auto-alignment system positioning accuracy of the image .When the axle differential is big the ellipse fitting based on least square method is improved to calculate the length of ellipse light spot major axis and minor axis, and to adjust the far field reflector to shape the light spot to get the regular circular spot, and then to calculate the deviation of circular light spot center and the reference center, which is transformed to the steps of closed-loop control stepping motor , achieving high power lasers beam auto-alignment. the algorithm is used in a high power laser facility auto-alignment system, the results show that the far field pointing accuracy is better than 0.033″, which is better than the original system.