In this study, a new signal-processing method was developed to improve the precision of locating flaw’s position using microwave NDT. The previous processing method is available only for the single-mode microwave, which causes the noise generation in the case that multi-mode microwaves propagate in a metal pipe. In order to reduce the noise, the reflections caused by the propagation of unintended modes were extracted and deducted from the original signal. The result showed the less noise intensity and higher signal-to-noise ratio than that without the procedure. After adopting this method, the flaw can be precisely located even under the interference of the undesirable modes.