Due to the existence of different stakeholders, it makes competitive game characteristic in hybrid energy systems (HESs). Combined with the high-dimensional complexity and output uncertainty of distributed energy resources, the optimal operation of HESs can be a more challenging problem. Here, this article proposes a potential game-based two-layered hierarchical optimization strategy to deal with this problem. With consideration of its high-dimensional complexity, a two-layered hierarchical HES model is created, consisting of an upper-level and a lower-level model. For properly solving competitive relationships among different stakeholders in the upper-level model, a multiagent system for stakeholders is created and a potential game is employed with a distributed primal-dual perturbed algorithm, and its convergence and optimality have been both proved. Moreover, an uncertainty and robustness analysis is done with coordination between lower and upper models, which deduces a feasible robust uncertainty interval in the lower-level model. For better dealing with the lower-level model, a gradient descent-based multiobjective differential evolution (GD-MODE) algorithm is utilized to optimize the economic cost and emission issue simultaneously, producing a set of Pareto-optimal schemes. Combined with simulation results, it is proven that the proposed method can reduce computational complexity as well as properly deal with uncertainty problems for the optimal operation of HESs.