The present invention relates to a control apparatus of a linear motion stage, which comprises: a first filter for filtering the frequency of a signal received from a linear encoder of the linear motion stage; an adder for adding an input signal representing a command position and a negative of an output signal of the first filter; a control for generating a control signal for controlling the linear motion stage based on an output signal of the adder; and a second filter for filtering the frequency of the control signal, wherein each of the input terminals of the first and second filters has a correction table for storing cut-off frequencies and damping rates measured according to the driven positions of the linear motion stage, thereby applying the correction table so as to determine the cut-off frequencies of the first and second filters and the damping rates according to the driven positions of the linear motion stage.
