Driven by global sulphur strategy, reducing sulfur emissions from the global shipping industry is of great significance for achieving sustainable development goals related to addressing climate change. This study explores the impact of government sulfur emission policies on the choice of mooring modes, include anchoring and drifting, for shipping lines. In this study, a bi-level programming model is constructed and linearized to minimize the total vessel emissions in emission control areas during the planning horizon and the total cost of each type of vessel. The leader of this model is the department that issues regulations and decides on the anchorage to regulate whether marine gas oil must be used. The followers are the shipping lines that execute transportation tasks and choose whether a vessel will anchor or drift. In addition, many numerical experiments and sensitivity analysis are conducted, and data and theoretical support for relevant decision-making are provided.