Integrated Energy Systems (IES) is critical for the sustainability in energy system development. But, the disturbances of different uncertainties and their propagation in the system make it hard to maintain a reliable service to the customers. To overcome this problem, a systematic method for the supply reliability analysis in IES is proposed in this work. In this method, the models of different units in the IES are developed considering their working mechanism and target functions. Then their random behaviours are based on their specified stochastic properties. And, their responses are integrated by a developed two-stage optimization model, to simulate the propagation of these events and to analyze the consequences in the system level. Finally, in the risk evaluation part, probabilistic and statistic descriptions are presented, and also a risk measure is adapted from Value at Risk, an important risk measure in financial analysis, for giving solid knowledge of the potential loss of service to the customers in terms of time duration, loss and probability. The effectiveness of this developed method is verified on an assumed IES. The results present its ability to give valuable information for design, extension and management of IES.