A method for estimating a variation in a preload applied to a linear guideway of a machine tool includes steps of: a) obtaining, via each of vibration sensors, first and second vibration signals that are generated according to detection of vibration of a table disposed on the linear guideway respectively at first and second time instants; b) determining, via the computation module, first and second natural frequencies based on a theoretical mode shape and respectively on the first and second vibration signals; and c) determining, via the computation module, the variation in the preload based on the first and second natural frequencies.