This study aims to discuss the dilemmas and solutions for the issues of high seas marine protected areas during the BBNJ negotiation. It expounds the dilemmas of BBNJ negotiations on the issue of MPAs (such as there is no single universally agreed definition of MPAs, the selection criteria for MPAs are still not clear and no clear consensus on the designation process of MPAs), analyzes the reasons for dilemmas of MPAs in the process of BBNJ negotiations and proposes the solutions of main issues in the process of BBNJ negotiations. The result of this research is that MPAs, as a breakthrough to the traditional marine management tools, are becoming an important means for the international community to protect marine biodiversity. Finally, it concluded that after dealing with dilemmas of lack of definition, unclear selection criteria and disputes over the governance model, the negotiation of the issue of MPAs in ABNJ will inevitably reach a reasonable institutional framework, and further promote marine biodiversity protection.