Double-flank measurement is the most widely used full inspection method in gear production workshops, which can obtain the radial composite deviation of gears. However, the double-flank measurements are usually affected by the error of the master gear. Correcting the error introduced by the master gear in double-flank measurements is an effective method to improve the application value of double-flank measurement. Based on the existing double-flank rolling tester, an error correction method for the master gear in double-flank measurement, based on changing the initial measurement teeth of the master gear and continuous rotation measurement was proposed. The corrected values of master gear error that can be applied to double-flank measurements are obtained. Multiple sets of simulation experiments with different radial composite deviations for the master gear and product gear are designed. The influence of radial composite deviation on double-flank measurements and the mechanism of the master gear error correction method are revealed. The consistency evaluation parameter that can reflect the accuracy of the double-flank measurement system is proposed to evauate the effectiveness of the error correction method. The measurement experiments show that, after using this method to correct double-flank measurements, the consistency of the center distance curve cluster measured from different phases of the master gear and the same phase of the product gear is significantly enhanced. Compared with before error correction, the consistency evaluation parameter shows that the accuracy of the double-flank measurement system has increased by 77.82%; compared with existing error compensation methods, the consistency evaluation parameter of the center distance curve cluster has been improved by 52.08%. The error correction method for master gear in double-flank measurement has effectively reduced the impact of the master gear error on the double-flank measurements. It has enhanced the traceability of double-flank measurements and the application value of double-flank measurement method, improved the accuracy of the double-flank measurement system, and enabled the double-flank measurements to more accurately characterize the quality of the product gear. Furthermore, this method exhibits superior performance in terms of measurement efficiency and the effectiveness of error correction.