To alleviate environmental pollution and improve the efficient use of energy, energy systems integration (ESI)-covering electric power systems, heat systems and natural gas systems-has become an important trend in energy utilization. The traditional power flow calculation method, with the object as the power system, will prove difficult in meeting the requirements of the coupled energy flow analysis. This paper proposes a generalized energy flow (GEF) analysis method which is suitable for an ESI containing electricity, heat and gas subsystems. First, the models of electricity, heat, and natural gas networks in the ESI are established. In view of the complexity of the conventional method to solve the gas network including the compressor, an improved practical equivalent method was adopted based on different control modes. On this basis, a hybrid method combining homotopy and the Newton-Raphson algorithm was executed to compute the nonlinear equations of GEF, and the Jacobi matrix reflecting the coupling relationship of multi-energy was derived considering the grid connected mode and island modes of the power system in the ESI. Finally, the validity of the proposed method in multi-energy flow calculation and the analysis of interacting characteristics was verified using practical cases.