In this paper, we propose a framework to design and analyze sustainability within complex multi-scale systems. Systems that have large variability in temporal and spatial resolution are common in lifecycle analyses and sustainability studies. Unlike traditional problems in systems engineering, these systems are composed of numerous interacting layers, each intricate enough to be a complete system on its own. In addition, the goal of achieving an economically and environmentally sustainable system introduces new elements to the problem domain. To manage this complexity, the suggested methodology focuses on integrating existing modeling constructs in a transparent manner, and capturing structural and functional relationships for efficient model reuse. The Systems Modeling Language (OMG SysML™) is used to formally implement the modeling framework. To demonstrate the method, we apply it to a large scale multi-modal transportation network. Analysis of key network parameters such as emissions output, well-to-wheel energy use, and system capacity are presented in a case study of the Atlanta, Georgia metropolitan area.