Aimed at diversity of hypersonic flight mission, multi-objective coordinated control of regeneratively-cooled scramjet engine with two-stage kerosene injection is discussed for guaranteeing a safe, steady and high-efficient operation. Firstly, characteristics analyses and system identification are conducted under the situation of flight Mach number 5 using unsteady 1-D model for regeneratively-cooled scramjet engine. Based on transfer functions obtained from system identification, corresponding proportional integral (PI) controllers are designed for different control objectives such as thrust, steady margin and kerosene temperature at cooling channels outlet. Secondly, different control strategies where flow rates of two stage kerosene injections are adjusted are created in different single control loops, including thrust regulation, steady margin protection, restart recovery, temperature protection and overtemperature recovery control loop. Optimal control strategy is determined ultimately in respective single control loop by analyzing merits and demerits from the perspectives of response speed and engine performance. Lastly, multi-loop coordinated control system is designed on the basis of switch rules and algorithm. Simulation results indicate that rapid responses of control system, smooth and steady switch between different loops are realized. Engine can operate steadily with high performance and recover to a safe operation state rapidly during unstart and overtemperature.