The transition to low and zero-emission transportation system marks a crucial paradigm shift, necessitating a reevaluation of resilience metrics and strategies. As infrastructure investments adapt to a changing climate and the risk of extreme events, our research identifies the complexities of resilience within the transportation sector, which now integrates a broad array of energy sources like electricity, hydrogen, and synthetic fuels. This deepening integration increases the complexity of maintaining transportation resilience, highlighting the inadequacy of traditional resilience metrics designed for centralized systems under stable climate conditions. Using a Multi-System Dynamics (MSD) framework, we propose to develop new, system-level resilience metrics to effectively manage emerging risks associated with diverse energy sources and extreme weather conditions. We emphasize the need for robust scenario analysis and the integration of Cost-Benefit Analysis (CBA) tools that account for resilience, offering a framework to evaluate the economic impacts and benefits of resilience investments. Our proposed approach encompasses evaluating resilience at the system level to identify and mitigate new risks introduced by the changing pattern of extreme events and the adoption of low-carbon technologies and the interconnectedness of modern energy and transportation infrastructures. Through rigorous scenario analysis, we aim to support robust decision-making that can withstand and adapt to the unpredictabilities and tipping points of a low-carbon future under changing climate conditions. By advancing these areas, we contribute to the strategic planning methodology necessary to foster a resilient, sustainable transportation ecosystem capable of facing both current and future challenges.