Due to the increasing adoption of smart and Internet of things (IoT) devices, Wind Energy System (WES) becomes more vulnerable to cyber- and physical-attacks. Therefore, designing a secure and resilient WES is critical. In this chapter, we first propose a System-of-Systems (SoS) framework for the cyber-physical WES. Specifically, on the one hand, we adopt a game-theoretic model to capture the interactions between the WES system defender and the adversary at the cyber-layer. The outcome of this cyber-defense game is reflected by control-aware Nash equilibria. On the other hand, we devise a cyber-aware robust and resilient switching controller based on a Markov jump linear system model for the physical WES. The performances of the WES cyber- and physical layers are interdependent due to their natural couplings. To design the integrated cyber-physical WES, we design an iterative algorithm to investigate the SoS equilibrium which considers the system security, robustness, and resilience in a holistic manner. Finally, we use case studies to corroborate the developed cross-layer design principles for the cyber-physical WES.