A method for preventing wafer surface from bombardment by micro-dust particles during the ion implantation process is disclosed. The method adjusts, in mobile way, the rotation direction of the rotating disk system in association with the inclined direction of the wafer to make the ion-implanting surface, having deep micro-size circuit structure, of the wafer never face the bombardment by the micro-dust particles during the rotation of the rotating disk system. The method includes: adjusting the rotating direction of the rotating disk into clockwise direction when it comes to performing an implantation at positive inclined angle; and adjusting the rotating direction of the rotating disk into counter-clockwise direction when it comes to performing an implantation at negative inclined angle. In this way, the ion-implanting surface of the wafer will never be bombarded by the micro-dust particles.