The conventional microwave transmission characterization of shock tube excited supersonic plasma, based on the equivalent complex propagation constant of plasma, is able to measure both electron density and electron neutral collision frequency from the amplitude and phase information of transmitted wave. However, the effects of reflected wave variations induced by plasma are usually neglected during the analysis, which can potentially cause unexpected deviations between the retrieved and actual states of plasma. 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.