In order to improve the precision and reliability of the spectral measurement of blood oxygen saturation, and enhance the validity of the measurement, the method of test analysis of variance was employed. Preferred wavelength combination was selected by the analysis of the distribution of the coefficient of oximetry at different wavelength combinations and rational use of statistical theory. Calculated by different combinations of wavelengths (660 and 940 nm, 660 and 805 nm and 805 and 940 nm) through the clinical data under different oxygen saturation, the single factor test analysis of variance model of the oxygen saturation coefficient was established, the relative preferabe wavelength combination can be selected by comparative analysis of different combinations of wavelengths from the photoelectric volume pulse to provide a reliable intermediate data for further modeling. The experiment results showed that the wavelength combination of 660 and 805 nm responded more significantly to the changes in blood oxygen saturation and the introduced noise and method error were relatively smaller of this combination than other wavelength combination, which could improve the measurement accuracy of oximetry. The study applied the test variance analysis to the selection of wavelength combination in the blood oxygen result measurement, and the result was significant. The study provided a new idea for the blood oxygen measurements and other related spectroscopy quantitative analysis. The method of test analysis of variance can help extract the valid information which represents the measured values from the spectrum.