With the optimization and transformation of the international cargo transportation system, building a comprehensive cargo transportation network led by container sea-rail intermodal transport has become a key focus of cargo transportation development at this stage. At the same time, the construction of the intermodal system still faces multiple challenges. From the perspective of actual production activities, the sea-rail intermodal transportation system has a high complexity of operations, low efficiency of container transshipment, which increases the operational costs of ports and the difficulty of rail access to the port. To address this challenge, this paper focuses on the optimization of the port operation system for sea-rail intermodal transportation. It delves into the analysis of the functional area configuration of sea-rail intermodal ports, conducts comparative analysis of different operation modes, and thereby selects the most suitable operation mode for the current development of intermodal ports.