While the spatial and functional relationships between ports and cities have been put in question in the last decades, the continued importance of urbanization and maritime transport in global socio-economic development motivates deeper research on their interaction. The global trade network is often studied at the country level and all transport modes included, concluding that distance remains a strong counterforce to exchange. This article wishes to detect whether the global container shipping network obeys similar properties at the city level. More than 2 million inter-port vessel movements between 1977 and 2016 are assigned to about 9000 ports and 4600 cities to run a gravity model on two different network topologies. Gravitational properties are found, as larger cities connect more with each other but less at distance. The degree of distance effects negatively expanded in 40 years, confirming the “puzzling” or reinforcing effect of distance, yet it varies greatly depending on node aggregation and network topology. We conclude that ports and cities continue to share important interdependencies, but these often rest on a detrimental physical transformation. A discussion is proposed about the underlying operational and theoretical mechanisms at stake.