The importance of rail-water intermodal transport is becoming more and more prominent in recent years. As a key node of rail-water intermodal transportation, the operation efficiency of automated container terminal directly affects the overall transportation efficiency. However, there are few studies on the collaborative scheduling of automated container terminal equipment in rail-water intermodal transportation. Therefore, this paper focuses on the ‘Automated Quay Crane (AQC)-Automated Straddle Carrier (ASC)-Automated Rail Mounted Gantry Crane (ARMG)’ operation system and addresses the operational efficiency requirements of the Automated Rail-Water Intermodal Transport Container Terminal (ARWITCT), Based on the bidirectional Hybrid Flow-shop Scheduling Problem (HFSP), a scheduling optimization model for the ARWITCT is established with the objective of minimizing the maximum completion time. To solve this complex scheduling problem, Particle Swarm Optimization based on Adaptive Tent Chaos Mapping (PSO-ATCM) is designed. In this algorithm, a parameter adaptive adjustment strategy and a Tent Chaos Mapping Optimization Strategy are introduced to help PSO jump out of local optimum. Problem-feature-based encoding and decoding methods are designed for the problem. An ‘insertion-translation’ mechanism is used to judge and resolve the conflicts between import and export containers during the decoding process. The effect of proposed scheduling model and the performance of the proposed algorithm are validated via comprehensive comparison experiments. To validate the effectiveness of proposed scheduling model, we compare the unidirectional HFSP model with the bidirectional HFSP model. The proposed PSO-ATCM is compared with standard Genetic Algorithm, Particle Swarm Optimization algorithm and Adaptive Genetic Algorithm. Computational results demonstrate that the proposed model is effective and PSO-ATCM performs better than other three compared algorithms.