This paper examines how spatial distance affects network topology on empirical data concerning the Global Container Shipping Network (GCSN). The GCSN decomposes into 32 multiplex layers, defined at several spatial levels, by successively removing connections of smaller distances. This multilayer decomposition approach allows studying the topological properties of each layer as a function of distance. The analysis provides insights into the hierarchical structure and (importing and exporting) trade functionality of the GCSN, hub connectivity, several topological aspects, and the distinct role of China in the network’s structure. It also shows that bidirectional links decrease with distance, highlighting the importance of asymmetric functionality in carriers’ operations. It further configures six novel clusters of ports concerning their spatial coverage. Finally, it reveals three levels of geographical scale in the structure of GCSN (where the network topology significantly changes): the neighborhood (local connectivity); the scale of international connectivity (mesoscale or middle connectivity); and the intercontinental market (large scale connectivity). The overall approach provides a methodological framework for analyzing network topology as a function of distance, highlights the spatial dimension in complex and multilayer networks, and provides insights into the spatial structure of the GCSN, which is the most important market of the global maritime economy.