The integrated energy system (IES) with hydrogen storage has become one of the most important developments in multi-energy coupling field, where the severe conflict of interests between different entities leads to great challenges to the economy and low-carbon operation. A multi-objective robust dynamic pricing and operation strategy optimization method based on the Stackelberg game is proposed for the hydrogen-containing energy storage (HES) IES. Firstly, the HES-IES trading framework is established based on the introduction of an integrated energy operator (IEO) and a load aggregator (LA). Secondly, a multi-objective robust Stackelberg game model is developed with the IEO as the leader and the LA as the follower, considering the minimization of operating costs and carbon emissions of the IEO and the minimization of integrated energy costs of the LA as the objectives. Finally, the compromise planning and the max-min fuzzy are addressed to solve the multi-objective model, which adopts the adaptive differential evolution (ADE) algorithm. In addition, the robust optimization (RO) with adjustable coefficients is employed to tackle uncertainties of source and load. The results show that this method can effectively balance the operating costs and carbon emissions of the system, improve the benefit of the IEO, reduce the costs of the LA, and avoid the uncertainty risk. Compared with traditional algorithms, the ADE algorithm has significant advantages in the number of iterations and solving time. In summary, the multi-objective robust dynamic pricing and operation strategy optimization proposed in this paper could effectively achieve the benefit balance between the IEO and the LA, also further improve the economy and robustness of the system and reduce carbon emissions.