The indoor one-kilometer projectile velocity measurement system cannot accurately identify the transonic projectile signal due to the interference signals generated by aerodynamics and other factors. To solve this problem, theoretical prediction of the projectile velocity at the transonic velocity measurement point is calculated by external ballistic numerical simulation technology based on the motion law of the center of projectile mass and the known measurement parameters of the indoor measurement system. In the measurement, a fast cross-correlation algorithm is used to process the projectile signals including interference signals and obtain velocity values at the measurement point. Then the theoretical prediction is used as the reference standard and the velocity with the smallest absolute value of the absolute error is selected as the desired measured value. A 5.8 mm rifle bullet is used to conduct an indoor one-kilometer live experiment. The results show that the relative errors between the measured value obtained by this method and the theoretical prediction are less than 1%, which eliminates the influence of interference signals and provides a new method for the accurate measurement of the transonic projectile velocity.