This paper focuses on the analysis of complex (multi-loop) energy-integrated process networks. Simple (single-loop) energy-integrated networks (comprising of large energy recycle or throughput) with two-time scale dynamics are the building blocks for such complex networks. The modular structure of these complex networks lends them to a graph theoretic analysis, whereby weak and strong connections between process units arising from time scale separation are identified from structural information. Subsequently, a graph-theoretic framework for network analysis and control is developed, and connecting links are built to an equivalent analysis using singular perturbations. The proposed analysis framework is illustrated via application to a representative complex process network. (C) 2015 Elsevier Ltd. All rights reserved.