Propelled by the “dual-carbon” strategy, green and intelligent ports are rapidly advancing toward low-carbon and intelligent development. However, the large-scale incorporation of renewable energy and the extensive electrification of transport equipment have substantially heightened system volatility and scheduling complexity. To address the challenges associated with multi-energy coupling and economic operation in medium and large ports, a hierarchical collaborative optimization scheduling strategy is proposed. The upper layer employs an improved Bio-enhanced Dung Beetle Optimization (BDBO) algorithm for parameter optimization and carbon-cost minimization. Meanwhile, the lower layer establishes a rolling time-series control mechanism grounded in Adaptive Dynamic Hierarchical Decoupling Planning (ADHDP), thereby constituting an integrated BDBO-ADHDP dual-agent system. Simulation results across four seasonal scenarios demonstrate that the proposed methodology outperforms DQN, PSO, GA, ACO, and DBO algorithms in reducing grid power purchases, enhancing renewable energy utilization, mitigating curtailment, and lowering operational costs. Moreover, it achieves faster convergence, superior robustness, and effective carbon-emission control. This study substantiates the efficacy of the proposed strategy within green port integrated energy systems and highlights its potential for broader application in other multi-energy coupled systems.