Integrated energy systems (IESs) can easily accommodate renewable energy resources (RESs) and improve the utilization efficiency of fossil energy by integrating various energy production, conversion, and storage technologies. However, the coupled multi-energy flows and the uncertainty of RESs bring challenges regarding optimal scheduling. Therefore, this study proposes an energy bus-based matrix-modeling method and a coordinated scheduling strategy for the IES. The matrix-modeling method can be used to formulate the steady- and transient-state balances of the multi-energy flows, and the transient model can clearly express the multi-time-scale characteristics of the different energy flows. The model parameters are fitted with data from experiments and the literature. To address the inherent randomness of the RESs and loads, a coordinated scheduling strategy is designed that contains two components: day-ahead optimization and rolling optimization. Day-ahead optimization uses the system steady-state model and multiple scenarios from the RES and load forecast data to minimize the operation cost while rolling optimization is based on the system’s transient-state model and aims to achieve the optimal real-time scheduling of the energy flows. Finally, a case study is conducted to verify the advantages and effectiveness of the proposed model and optimization method. The results show that stochastic optimization reduces the total daily cost by 1.48% compared to deterministic optimization when considering the prediction errors associated with the RESs and loads, highlighting the stronger adaptability of stochastic optimization to prediction errors. Moreover, rolling optimization based on the system’s transient-state model can reduce the errors between day-ahead scheduling and rolling correction.