Thermal choke is commonly employed in a fixed geometry RBCC combustor to eliminate the need for physically variable exit geometry. This paper proposed detailed numerical studies based on a two-dimensional integration model to characterize thermal choke behaviors driven by various embedded rocket operations in an RBCC engine at Mach 4 in ramjet mode. The influences of different embedded rocket operations as well as the corresponding secondary fuel injection adjustment on thermal choke generation process, the related thermal throat feature, and the engine performance are analyzed. Operations of embedded rocket bring significant effects on the thermal choke behaviors: (1) the thermal throat feature becomes much more irregular influenced by the rocket plume; (2) the occupancy range in the combustor is significantly lengthened; (3) the asynchrony of the flow in different regions accelerating to sonic speed becomes much more significant; (4) as the rocket throttling ratio decreases, the thermal choke position constantly moves upstream integrally, and the heated flow in the top region that is directly affected by the rocket plume reaches sonic speed more rapidly. Finally, we can conclude that appropriate secondary fuel injection adjustment can provide a higher integration thrust for the RBCC engine with the embedded rocket operating, while the thermal choke is stably controlled, and the increased heat release and combustion pressure are well balanced by the variations of pre-combustion shocks in the inlet isolator.