Developments in nanotechnology have led to innovative progress and converging technologies in engineering and science. These demand novel methodologies that enable efficient communications from the nanoscale all the way to decision-making criteria for actual production systems. In this paper, we discuss the convergence of nanotechnology and novel multi-scale modeling paradigms by using the fuel cell system as a benchmark example. This approach includes complex multi-phenomena at different time and length scales along with the introduction of an optimization framework for application-driven nanotechnology research trends. The modeling paradigm introduced here covers the novel holistic integration from atomistic/molecular phenomena to meso/continuum scales. System optimization is also discussed with respect to the reduced order parameters for a coarse-graining procedure in multi-scale model integration as well as system design. The development of a hierarchical multi-scale paradigm consolidates the theoretical analysis and enables large-scale decision-making of process level design, based on first-principles, and therefore promotes the convergence of nanotechnology to sustainable energy technologies.