The design and operation of integrated energy systems requires considering the interaction between multiple infrastructures, each with its distinctive features. For instance, the network topology and the physical phenomena involved in the transmission of different energy vectors hugely affect the energy flows, impacting the efficiency and vulnerability of the energy grid as a whole. Graph-theoretical complex network analysis, and specifically multilayer networks, provide a powerful modelling technique to assess the interdependence between different energy infrastructures. The relevance of this integrated approach becomes evident as the number of installed energy converters, such as cogenerators, fuel cells and electric heat pumps, increases and affects the energy flows across these infrastructures. In this chapter, complex network analysis, commonly employed for individual energy networks, is extended to multi-energy systems, modelled as multilayer networks interacting through energy hubs. The case study, based on a benchmark power grid coupled with a gas network, demonstrates the capabilities of multilayer networks to model multi-energy systems and detect hidden features arising from the interdependence between multiple energy carriers.