Liner shipping accounts for over 80% of the global transportation volume, making substantial contributions to world trade and economic development. To advance global economic integration further, it is essential to link the flows of global liner shipping routes with the complex system of international trade, thereby supporting liner shipping as an effective framework for analyzing international trade and geopolitical trends. Traditional methods based on first-order global liner shipping networks, operating at a single scale, lack sufficient descriptive power for multi-variable sequential interactions and data representation accuracy among nodes. This paper proposes an effective methodology termed “Multi-Scale Higher-Order Dependencies (MSHOD)” that adeptly reveals the complexity of higher-order interactions among multi-scale nodes within the global liner shipping network. The key step of this method is to construct high-order dependency networks through multi-scale attributes. Based on the critical role of high-order interactions, a method for key node identification has been proposed. Experiments demonstrate that, compared to other methods, MSHOD can more effectively identify multi-scale nodes with regional dependencies. These nodes and their generated higher-order interactions could have transformative impacts on the network’s flow and stability. Therefore, by integrating multi-scale analysis methods to mine high-order interactions and identify key nodes with regional dependencies, this approach provides robust insights for assessing policy implementation effects, preventing unforeseen incidents, and revealing regional dual-circulation economic models, thereby contributing to strategies for global, stable development.