Today’s increasingly complex energy systems require innovative approaches to integrate and optimize different energy sources and technologies. In this paper, we explore the system of systems (SoS) approach, which provides a comprehensive framework for improving energy systems’ interoperability, efficiency, and resilience. By examining recent advances in various sectors, including photovoltaic systems, electric vehicles, energy storage, renewable energy, smart cities, and rural communities, this study highlights the essential role of SoSs in addressing the challenges of the energy transition. The principal areas of interest include the integration of advanced control algorithms and machine learning techniques and the development of robust communication networks to manage interactions between interconnected subsystems. This study also identifies significant challenges associated with large-scale SoS implementation, such as real-time data processing, decision-making complexity, and the need for harmonized regulatory frameworks. This study outlines future directions for improving the intelligence and autonomy of energy subsystems, which are essential for achieving a sustainable, resilient, and adaptive energy infrastructure.