To improve energy efficiency and reduce pollution emissions of ports with electricity and hydrogen substitution, this paper proposes a collaborative scheduling method of port integrated energy and container logistics considering electric and hydrogen-powered transport. By analyzing the coupling relationship between energy production and consumption in a port that deploys electric and hydrogen-powered transport, the scheduling optimization models of the port integrated energy system (PIES) and the port container logistic system (PCLS) are collaboratively established and rendered as a mixed-integer bi-level programming model. Moreover, to simplify the complexity of PCLS scheduling which involves the allocation and operation of each type of container logistics equipment, an assembly line of port container logistics (ALPCL) model based on flexible job-shop scheduling (FJSS) is further constructed. Then, a distributed algorithm based on the Benders decomposition (BD) embedded with an improved non-dominated sorting genetic (INSGA-II) is designed to realize optimal dispatch with limited data exchange and great solution efficiency. The results of case studies demonstrate the effectiveness of the proposed method for economic and environmental benefits, including a reduction in scheduling costs and pollution emissions. This method can also achieve co-improvement of energy and logistics efficiency