Turbine-based combined-cycle (TBCC) propulsion systems have been a topic of research as a means for more efficient flight at supersonic and hypersonic speeds. The present study focuses on the fundamental physics of the complex flow in the TBCC exhaust system during the transition mode as the turbine exhaust is shut off and the ramjet exhaust is increased. A TBCC exhaust system was designed using methods of characteristics (MOC) and subjected to experimental and computational study. The main objectives of the study were: (1) to identify the interactions between the two exhaust jet streams during the transition mode phase and their effects on the whole flow-field structure; (2) to determine and verify the aerodynamic performance of the over-under TBCC exhaust nozzle; and (3) to validate the simulation ability of the computational fluid dynamics (CFD) software according to the experimental conditions. Static pressure taps and Schlieren apparatus were employed to obtain the wall pressure distributions and flow-field structures. Steady-state tests were performed with the ramjet nozzle cowl at six different positions at which the turbine flow path were half closed and fully opened, respectively. Methods of CFD were used to simulate the exhaust flow and they complemented the experimental study by providing greater insight into the details of the flow field and a means of verifying the experimental results. Results indicated that the flow structure was complicated because the two exhaust jet streams interacted with each other during the exhaust system mode transition. The exhaust system thrust coefficient varied from 0.9288 to 0.9657 during the process. The CFD simulation results agree well with the experimental data, which demonstrated that the CFD methods were effective in evaluating the aerodynamic performance of the TBCC exhaust system during the mode transition.