For measurement of existing thread parameters using profile scanning, system error increases as pitch diameter, difference between the calibrating thread and measuring thread increases with the single gauge calibration method. There are several alignment deviations affecting the measurement of pitch diameter. To reduce the system error, a compensation method using two standard thread gauges to calculate the alignment deviations is proposed here. Finally, the theoretical and experimental comparisons between the single gauge calibration method and the proposed method are presented. The results demonstrate that the two gauges calibration method can effectively reduce the system error.