This paper is concerned with the control and optimization of ignition transient and flame development in a scramjet engine using air throttling. The control scheme is based on a quasi-one-dimensional model of unsteady reacting flow motion, which reasonably simulates the ignition process and ensuing flow evolution in a scramjet engine with a cavity flameholder. The model has been validated against measured pressure data for cases involving gaseous ethylene. A parametric study is conducted to investigate the influences of all known effects (such as location and operation timing of air throttling, fuel injection, and ignition duration) on the characteristics of engine ignition transient. Optimization of air throttling is achieved using the genetic algorithm (GA).