This book adopts a systematic view of the control systems in cyber-physical systems including the security control of the optimal control system, security control of the non-cooperative game system, quantify the impact of the Denial-of-Service attacks on the optimal control system, and the adaptive security control of the networked control systems. Because the cyber-physical system is a hybrid system, it adopts cross layer approach to handle the security control of the CPS. It presents a number of attack models according to the attack scenario and defense facilities, and a number of cross-layer co-design methodologies to secure the control of CPS.