A simplified configuration was developed to facilitate the mode transition process within an over-under Turbine-Based Combined Cycle (TBCC) inlet. Leveraging dynamic mesh technology, an unsteady numerical simulation of the mode transition was conducted, emphasising the flow characteristics of the mode transition and the impact of key similarity criteria numbers. The findings indicate that at an incoming Mach number of 2.0, the mode transition is paired with a continuous alteration in the capture mass flow of the high-speed duct. This continual change instigates the inlet unstarting, with subsequent flow characteristics being contingent on the historical effect, exhibiting a degree of hysteresis characteristics. When the scale effect is considered, it is observed that a larger model scale results in higher Reynolds (Re) and Strouhal (St) numbers. This directly contributes to a notable delay in the unstart moment, a decrease in the unstart interval, and an enlargement of the hysteresis loop. An examination of control variables reveals that the Re number marginally influences mode transition characteristics, while the St number’s effect constitutes approximately 90% of the scale effect. This conclusively demonstrates that the St number is the predominant similarity criterion number in the mode transition process.