This dissertation studies the analysis and design of Cyber-physical Systems (CPS) using passivity and passivation theory, concentrating on applications in automotive systems. Passivity and dissipativity have shown great promise in the design of CPS due to many properties they can provide, such as stability, robustness and compositionality. The main contributions of this dissertation are summarized as follows. First, we show that passivity and dissipativity properties of a system can be implied from its approximate models given that the model is 'close' to the system dynamics in a suitably defined sense. To illustrate, we consider approximation methods such as linearization, model reduction, discretization and quantization. Second, to apply passivity-based control, we use a passivation method that can guarantee desired passivity levels for the system. The passivation method allows the use of a non-passive controller to stabilize or passivate another plant. In particular, the passivation method can be applied to systems with input-output delay, such as human operators. Third, when control algorithms are implemented in software, delays cannot be avoided. The passivation method can be applied in order to guarantee stability and optimize system performance in the presence of time delay. As an application, we study the passivation method in adaptive cruise control design for automotive systems. Finally, we consider a state estimation problem in CPS where multiple processes share the communication medium. We analytically calculate the performance expressions for time-triggered and event-triggered schemes under various contention resolution mechanisms. The result demonstrates that a simple time-triggered scheme may perform better than an event-triggered scheme when the effects of the communication strategies are explicitly considered. In summary, this dissertation focuses on the analysis and design of CPS using passivity and passivation theory, concentrating on systems with human controllers and automotive systems.