The present invention discloses a method and apparatus for eliminating interference in pulse oxygen measurement. The method comprises the steps of: collecting a first wavelength light and a second wavelength light transmitting through the object to be measured and converting collected optic signals into electric signals to form a plethysmogram; processing the plethysmogram so as to normalize it, in order to decompose the normalized plethysmogram into a combination of an ideal plethysmogram and noise, and expand the ideal plethysmogram by using functions that can make up a complete orthonormal system; eliminating the noise in the plethysmogram through differential operation; and restoring the plethysmogram free of noise through integral operation for calculating oxygen saturation. The apparatus comprises a collecting module, a processing module, a noise eliminating module, and a restoring module. The method and apparatus suitable for the measurement of oxygen saturation under weak perfusion and movement conditions.