A controlling method of an encoder includes: detecting a rotation angle of a rotor of a motor coupled to the encoder to generate a first counting trigger signal and a second counting trigger signal so as to perform a turn number counting procedure; determining whether a period that an operating voltage of a driving circuit of the motor is smaller than a threshold voltage exceeds a preset time; and when the period exceeds the preset time, controlling a switching unit of the encoder to allow a battery of the encoder to provide a backup voltage to the encoder such that the encoder enters a low power processing procedure.