As a key enabler of international trade, the container shipping market experienced port congestion, space shortages, and skyrocketing freight rates following the outbreak of the COVID-19 pandemic. Therefore, this paper first utilizes the vector autoregressive model with exogenous variables (VARX) to analyze the interactive mechanisms of economy, capacity, freight rate, and port congestion during the pandemic to identify the causes behind the excessive market volatility. We then introduce government supervision to improve the policy deficiencies in pricing rules and assess whether prohibiting liner companies from charging excessive surcharges can solve market dilemmas by constructing a tripartite evolutionary game model. The results show that liner companies deliberately maintained congestion by using strict control over shipping capacity to raise freight rates and obtain high profits, which is one of the main reasons for the problems. However, we also conclude that relying solely on the spontaneous behavior of the market is unlikely to resolve the predicament. Instead, government intervention can play a crucial role in encouraging liner companies to increase appropriate container capacity, stabilize freight rates, and mitigate the risk of supply chain disruptions due to port congestion. This, in turn, can enhance the resilience of the container transport system.