In this work, the theoretical analysis and experiment results investigating the influence of plasma-induced reflected wave variations on microwave transmission characterization are presented. Firstly, an analytical transmission line model for transmission characterization of plasma in shock tube is derived and validated against full-wave simulation. Then, the theoretical analysis of transmission characterization based on a time-dependent reconstruction algorithm that takes into account the variations of reflected wave is presented and the influence of reflection variations under various states of plasma is also investigated. The unusual increase in the amplitude of transmitted wave is theoretically predicted and experimentally demonstrated as well. Finally, the experiment results are also presented to illustrate the effects of reflected wave variations in practical microwave transmission characterization of supersonic plasma excited in shock tube.