In order to reduce the influence of uncertainty on both sides of the source and load on the security and economy of the integrated energy system (IES), and to improve the flexibility and stability of IES in the face of uncertainties, various strategies for energy storage participation in smoothing out the uncertainty fluctuations are proposed, and a robust model is established for the day-ahead and real-time two-stage cooperative optimization under multiple uncertainties. A robust adjustable factor is added to the model to comprehensively evaluate the system economy and robustness. In the day-ahead phase, a pre-dispatch plan is determined based on the predicted power of new energy and load to realize the power balance at the minimum operating cost. In the real-time phase, the adjustment power of the secondary flexible adjustment equipment is determined according to the new energy output and the actual simulated power of the load to realize power rebalancing at minimum cost. The case study shows that the real-time adjustment of power supply side and energy storage side can better play the synergistic adjustment function of IES to deal with uncertainty; the introduction of robust adjustable factor to portray the uncertainty better balances the economy and security of system operation.