This study examines global container ports' vulnerability to natural disasters by integrating perspectives from the hinterland, port interface, and seaside network, which is crucial but has been absent from existing literature. A port vulnerability index is first constructed utilizing daily shipping traffic data at 735 container ports worldwide and coordinates data of 1,768 natural disasters between 2015 and 2019. Subsequent causality analyses reveal that port vulnerability is inversely related to port infrastructure development, hinterland industrial diversity, and port connectivity in the global shipping network. Additionally, the heterogeneity tests show that the influence of these determinants on port vulnerability varies by regional economic levels and disaster types. We address the endogeneity problem arising from reverse causality between industrial diversity and port vulnerability, and between port connectivity and port vulnerability respectively. These findings provide novel insights and approaches for policymakers and port authorities, further enhancing global trade and economic resilience. The heterogeneous test results, in particular, offer guidance on prioritizing policies when resources are limited.