For enhancing the performance of automated container terminals, this PhD thesis focuses on improving energy efficiency and implementing more autonomous equipment (e.g., free-ranging AGVs) at the operational level. On the one hand, due to the increased energy price and environmental stress, energy efficiency needs to be improved. On the other hand, new emerging AGVs allow free-ranging behavior and can shorten the driving distance than using the traditional routing strategy, demanding a novel advanced control algorithm for scheduling and controlling the free-ranging AGVs and the other related machines. For achieving these research goals, both discrete-event dynamics and continuous-time dynamics are considered in this thesis, using a perspective of hybrid systems. Simulation experiments on compact, medium and large-scale terminal case studies show the potential of the proposed new approaches.