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While the Biodiversity Beyond National Jurisdiction (BBNJ) Agreement establishes a comprehensive environmental impact assessment (EIA) regime, its application of the EIA provisions to the international seabed area (the Area) presents significant challenges. First, International Seabed Authority (ISA) Member States have differing ratification and signature statuses regarding the BBNJ Agreement, leading to fragmented and asymmetrical obligations. Second, normative ambiguity surrounds the “not undermine” proviso, and an institutional disconnection exists between the Clearing-House Mechanism under the BBNJ Agreement and the ISA. Third, the “equivalence exception” under Article 29(4) of the BBNJ Agreement generates a critical interpretive dilemma. The absence of institutional mechanisms for determining equivalence risks unilateral self-assessment and forum-shopping. Furthermore, substantive disparities exist between the BBNJ Agreement and ISA regulations, particularly regarding the screening process, Cumulative Environmental Effects, and Strategic Environmental Assessment, alongside asymmetries in procedural transparency and stakeholder engagement. Finally, an empirical analysis reveals that the EIA practices in the Area remain scarce and inaccessible, and existing Environmental Impact Statements appear not fully aligned with the standards prescribed by Article 33(2) of the BBNJ Agreement. Therefore, this article puts forward recommendations to optimize the application of the EIA provisions under the BBNJ Agreement. First, concerted efforts must be made to advance the ratification and accession of the BBNJ Agreement by ISA Member States. Second, the “not undermine” proviso should be interpreted narrowly to ensure the BBNJ Agreement’s implementation does not actively dismantle the effectiveness of the ISA. Third, Parties should facilitate the determination of equivalence through harmonization and scientific advice, leveraging the supplementary role of the Scientific and Technical Body. Fourth, cooperation must be formalized through institutional frameworks, specifically by signing a Memorandum of Understanding and enhancing inter-institutional expert consultation. Finally, stakeholders must enhance EIA practices by standardizing the mechanism for updating reports and ensuring that dual-member States comply with the standards of both regimes.