Shipping alliances are regarded as a special group in antitrust immunity policies worldwide because of their abilities to coordinate shipping resources. In particular, the international shipping involves different countries and stakeholders, making it difficult to form a unified antitrust immunity and maritime policy. This study builds a tripartite dynamic evolutionary game model composed of stakeholders including the shipping alliances, ports, and governments. It analyses the complex impacts of government policy, cooperation between the port and shipping alliance, accountability mechanism, and sudden changes in the external environment on the different stakeholders’ decisions. The stability points, evolution process, and evolution speed of the tripartite game, along with the movement of the convergence point in the unstable state, are investigated. Furthermore, the mutual influence of the three parties, especially that of government policy on the evolution process regarding the pricing strategy and antitrust immunity, is discussed. The results show that the reduction in the freight rate difference makes it easier for the alliance to choose a low-freight strategy under the antitrust immunity policy. The government could cooperate with the port and indirectly restrict the alliance through the port extra charge, while an increase in the alliance supply would weaken the port’s bargaining power. This research also investigates the timing of government regulation by considering the sudden fluctuations of the market and the international political risk when the three parties exert a push–pull pressure on one another’s decisions and provides comprehensive decision support for the three parties from the perspective of dynamic evolution.