Hayabusa spacecraft autonomously performed a terrain alignment maneuver that accomplished both altitude and attitude control whose reference was the surface itself. Hayabusa spacecraft was equipped with four beams Laser Range Finder (LRF) onboard. LRF played a very important role to control its position and attitude at the very low altitude, when the spacecraft was out of remote control and was supposed to perform this task pure autonomously. Actually, Hayabusa spacecraft hovered with this method at 17 meters high at the first touching-down attempt and at 7 meters high at the second touching-down attempt. This paper presents how these autonomous controls were performed in detail.