To improve the operating efficiency of U-shaped automated container terminal and to promote the development of green port, aiming at the loading and unloading process of dual trolley quay crane + Automated Guided Vehicle (AGV) + dual cantilever rail crane + external truck, considering the uncertainty of external truck arrival, a green waiting strategy was proposed by using the related theory of hybrid flow shop scheduling. With the goal of minimizing the completion time of all tasks and minimizing carbon emission of operating equipment, a multi-objective green integrated scheduling model was constructed and an improved hybrid genetic cuckoo algorithm was designed to solve the model. Through small, medium and large-scale container operation task experiments, the proposed algorithm was compared with genetic algorithm, adaptive genetic algorithm and grey wolf optimizer algorithm to verify its effectiveness. The results showed that the result of no wait strategy was better when the task size was small, and with the increase of task size, the difference between them decreased gradually. When the task scale was large, the result of waiting strategy was better. © 2022 CIMS. All rights reserved.