A system and a method for moving a wafer during scanning the wafer by an ion beam. The proposed system includes an extendable/retractable arm, a holding apparatus and a driving apparatus. At least a length of the extendable/retractable arm is adjustable. The holding apparatus is capable of holding a wafer and is fixed on a specific portion of the extendable/retractable arm. Furthermore, the driving apparatus is capable of extending and/or retracting the extendable/retractable arm, such that the holding apparatus is moved together with the specific portion. In addition, the proposed method includes the following steps. First, hold the wafer by a holding apparatus fixed on a specific portion of an extendable/retractable arm. After that, adjust a length of the extendable/retractable. Therefore, the holding apparatus, i.e. the wafer, can be moved by the extension/retraction of the extendable/retractable arm.