Difficulties in achieving efficient ignition and steady combustion in a high-speed environment have long been serious concerns in the development of scramjet engines. The situation becomes more challenging during the engine start-up stage when the low chamber pressure and unsettled fuel-air mixing tend to blow off the flame, even if a flame holding device such as a cavity is employed. One of the ignition aids is to modulate the flow structures in the isolator and combustor by means of air throttling downstream of the flame holder, in order to reduce the local flow velocity and increase the pressure. The purpose is to establish a proper shock train in the isolator to facilitate ignition and flame stabilization. In experiments, compressed air is introduced in a controlled manner into the combustor to generate a pre-combustion shock train in the isolator. The resultant increases in the temperature and pressure of the air stream in the combustor, along with the decrease in the flow velocity, lead to smooth and reliable ignition. The shock train also gives rise to lowmomentum regions and separated flows adjacent to the combustor side-wall. The fuel-air mixing process in separated flows is considerably enhanced due to shock-induced flow distortion and large residence time. In general, air throttling is activated once steady fuel injection has been achieved and an ignition source such as a spark-plug has been turned on. Air throttling is terminated immediately after the flame is stabilized, in order to minimize the amount of throttling gas. If the subsequent heat release in the combustor is sufficiently high, a proper shock system in the isolator for sustaining combustion is maintained. Insufficient heat release often leads to an unstable shock train. A premature removal of air throttling may result in flame blowout. It should also be noted that the shock train interacts with the inlet flow field. Significant flow spillage or even inlet unstart may occur if the combustor is over pressurized. A dynamic optimization of the shock train is needed to ensure smooth ignition and flame stabilization. The present work establishes an integrated theoretical/numerical framework within which the influences of all known effects (including the location and operating timing of air throttling and fuel injection) on the engine ignition transient and flame development are studied systematically.