This article investigates the impact of container yard layout on the cargo handling time of intermodal trains operating at container terminals, with a particular emphasis on the number of stacking layers used in container storage. The study focuses on how varying vertical storage configurations influence the duration of crane loading cycles as well as the energy consumption of transshipment equipment. In addition to the stacking layout, the analysis incorporates several operational constraints that are critical in intermodal rail transport, including the locking pin arrangements on railcars, container gross weights, and axle load limitations specific to intermodal wagons. The theoretical section outlines the fundamental role of intermodal terminals within global logistics and supply chains. It delves into the organization of container storage within terminal yards, highlighting its influence on handling performance and the overall turnaround time of intermodal transport units. Furthermore, the article includes a comprehensive literature review that examines state-of-the-art research on container yard storage strategies, allocation rules, and various optimization approaches aimed at improving yard efficiency. To evaluate the operational impact of different stacking strategies, a simulation model was developed using the FlexSim platform. The model allows for detailed analysis of crane cycle times in relation to stacking configurations, while also accounting for the energy usage of cranes and handling equipment. The simulations were carried out for a range of stacking scenarios to reflect real-world variability and constraints encountered in container terminals. The findings reveal that the relationship between the number of stacking layers and train loading time or energy consumption is non-linear and often counterintuitive. Increasing the number of layers does not necessarily lead to proportional gains or losses in efficiency. Instead, certain configurations may result in operational bottlenecks or increased energy use due to additional crane repositioning and container relocations. The research not only provides quantitative evidence on the operational consequences of yard design decisions but also offers practical insights for terminal planners and operators. These insights can support both short-term operational planning and long-term strategic investments aimed at optimizing terminal performance and sustainability.