The COVID-19 pandemic has severely impacted international economics and trade, including cargo transportation. As a result, enhancing the resilience of transport and logistics in the post–COVID-19 era has become a general trend. Multimodal transport, with its advantages of speed, large volume and multiple modes, has increasingly gained attention from countries worldwide. However, multimodal transport logistics is a complex and systematic process. Its smooth flow depends not only on the transport itself, but also on the efficient supervision of customs and other government departments at ports. This study employs the theory and method of a super-network to establish a model of multimodal transport logistics, which includes TIR-based sea–road multimodal transport and customs supervision relationships. Structural and resilience-related characteristics of the super-network are analyzed, and performance parameters of the super-network are proposed. A simulation analysis is conducted, and based on the results, countermeasures to improve the resilience and promote risk management of multimodal transport logistics in the post–COVID-19 era are suggested. The findings of this study provide an exploration of more effective ways to ensure the smoothness of multimodal transport logistics and improve system resilience. The study concludes with theoretical and managerial implications.

Collaborative governance of ports along the 21st Century Maritime Silk Road (MSR) is persistently constrained by low community participation and fairness disputes among the government, enterprises, and local communities. Conventional governance models assume fully rational actors and thus neglect pervasive fairness preferences of these three stakeholder groups. To fill this gap, we develop a tripartite evolutionary game model embedding fairness preferences. The model introduces three coefficients—α for the government, β for enterprises, γ for local communities—and distinguishes competitive preferences from social welfare preferences. The model systematically analyzes evolutionary stable strategies under different preference combinations, followed by numerical simulations based on the Piraeus Port case. The results show that: (1) Material incentives alone exhibit threshold effects and structural limitations: when insufficient, the system stabilizes at a binary cooperation state (the government promotes, enterprises cooperate, local communities oppose), denoted as (1,1,0). (2) Local communities’ social welfare preference (γ > 0) alone can tip the system toward full tripartite cooperation (1,1,1). (3) Competitive preferences typically impede cooperation, whereas aligned social welfare preferences across all three parties constitute the most favorable condition for collaborative governance. (4) Strategy evolution displays differential sensitivity: local communities’ fairness preference is the critical lever, government preference remains largely neutral, and enterprises’ competitive preference has the strongest destabilizing effect. Based on these findings, the paper proposes policy strategies including reputation constraints, cost-sharing and benefit-sharing mechanisms, optimized transfer payments and spillover structures, and normalized consultation mechanisms. These findings provide a behavioral-theoretical foundation for advancing MSR port governance from binary cooperation to tripartite synergy.