In view of the limitations of the existing eccentricity error separation method of the rotary table, an eccentricity error separation method based on the phase feature of the moiré signal of single reading head is proposed herein. A grating pair transmission model is established based on the analysis of the principle of the rotary table, thereby the influence of eccentricity error on the phase feature of the moiré signal in the rotation course of the rotary table is clarified, and the corresponding model between the phase feature spectral components and the eccentricity error is established. The verification experiments of the proposed method are carried out based on the laboratory-made circuit system. After verifying the accuracy of the data acquisition of the laboratory-made circuit board, the verification experiments of the eccentricity error separation effect of the proposed method are carried out. The experimental data are compared with those of the traditional method and the results show that the error between the two methods is 2.34μm and the relative error is 2.3%.