Multiple energy systems (MESs) bring together the electric power, heat, natural gas, and other systems to improve the overall efficiency of the energy system. An energy hub (EH) models an MES as a device with multiple ports using a matrix coupling the inputs and outputs. This paper proposes a standardized matrix modeling method based on the concept of EH to build the coupling matrix automatically. The components and the structure of MES are first defined using graph theory. Then, the matrices describing the topology of the MES and the characteristics of the energy converters are developed. On this basis, the energy flow equations are formulated. Gaussian elimination can then be applied to obtain the coupling matrix and analyze the degree of freedom of the EH. A standard data structure for basic information on the MES is proposed to facilitate computerized modeling. Further, extension modeling of energy storage and demand response is also discussed. Finally, a case study of a modified tri-generation system is conducted to illustrate the proposed method.