Deep-sea aquaculture is an important tool to expand the production space of “blue granary”，and clarifying its synergy mechanism is the basis for ensuring the high-quality development of deep-sea aquaculture. Based on the stakeholder theory，identify the stakeholders of deep-sea aquaculture and build a synergistic mechanism including a synergistic motivation mechanism，synergistic operation mechanism，synergistic guarantee mechanism，and synergistic realization mechanism. The study studied how stakeholders such as government，enterprises，and research institutions can synergize in terms of institutions，technology，and funding，so that aquaculture activities，technology research and development，and production and marketing linkages can be dynamically adjusted to different realities，and institutional safeguards can be used to promote deep-sea aquaculture to a higher stage of quality development. The “Yellow Sea Cold Mission Green and Efficient Fish Aquaculture Project” was selected as a typical case study，and the results show that the project management system has been continuously standardized，reflecting the synergistic mechanism of government-led participation of multiple entities. The financial，technical，and institutional support should be further strengthened in the future to support the efficient operation of the project，which will provide a reference for the high-quality development of deep-sea aquaculture.