The present invention relates to an apparatus for eliminating motion artifacts and a method thereof, and the method for eliminating motion artifacts includes steps of receiving a PPG signal and three-axis (X-axis, Y-axis, and Z-axis) acceleration signals measured from an examinee, extracting the PPG signal and the three-axis acceleration signals by a period of a predetermined unit of time and filtering the signals at a preset bandwidth, Fourier-transforming the PPG signal and the three-axis acceleration signals corresponding to the extracted period, arranging power spectra of the X-axis, Y-axis, and Z-axis in ascending order of value of average power spectrum by calculating an average power of each frequency domain of the three-axis accelerations, and extracting a final power spectrum of the PPG signal by sequentially eliminating power spectra of the X, Y, and Z-axis accelerations from the power spectrum of the PPG signal in an order of arrangement.