This paper focuses on the analysis of complex material integrated plants, which may consist of multiple interconnected recycle structures, with material flows spanning multiple orders of magnitude. For such plants, there is a potential of exhibiting multiple time scale material dynamics. An analysis framework is developed to identify the time scales where each process variable evolves and the potential manipulated inputs available in each time scale. A novel graph formalism is proposed to capture the material flow structure of such plants. Then, a graph-theoretic algorithm is developed, which mimics a singular perturbation-based time scale decomposition. The application of the proposed framework is illustrated using two example chemical plants.