Clean hydrogen is globally recognized as essential for decarbonization, yet its environmental value is not inherent; it is a legal status requiring robust certification. This article addresses Thailand’s subsidy paradox, where ambitious climate goals and Board of Investment (BOI) incentives for clean hydrogen are rendered functionally inoperable. This paralysis stems from a critical legal gap: the absence of a national definition, standard, and verification system for clean hydrogen, which creates severe legal uncertainty for investors. The research argues that certification is a foundational legal prerequisite for any subsidy regime. Employing a functional-structural comparative legal methodology, the study analyzes six key jurisdictions (the United States, Canada, the European Union, South Korea, Australia, and Japan) to identify international best practices. Findings reveal an alignment on technical criteria (e.g., Well-to-Gate greenhouse gas assessment scope, tiered thresholds up to 4.0 kgCO2e/kgH2), but finds Thailand’s current legal framework (BOI, ERC, TISI) incompatible for implementation due to critical jurisdictional and institutional constraints. The article concludes that the enactment of a new law is essential, recommending the enactment of a sui generis Hydrogen Certification Act. This new legal framework should adopt a pragmatic hybrid model, blending South Korea’s tiered, technology-neutral, Well-to-Gate criteria with Australia’s flexible, unbundled certificate (PGO/REGO) structure. This approach provides legal certainty while avoiding the prohibitive complexity of the EU model.