This study re-conceptualizes Japan’s trade negotiations with the United States in the era of economic security as a “Third Strategic Option,” and analyzes the structural characteristics and strategic coordination mechanisms of Japanese trade diplomacy. Employing an analytical framework that integrates complex interdependence and two-level game theory, the study demonstrates that Japan’s trade policy operates through a triple-binding architecture linking the international (alliance management and multilateral rule-making), domestic (interest groups and bureaucratic politics), and institutional (legal, fiscal, and supply chain frameworks) dimensions. Reconstructing the post-2018 negotiation process into the stages of pressure formation, bargaining, compromise, and institutional stabilization, the analysis identifies a sectorally differentiated portfolio of selective autonomy expansion—managed concessions in agriculture, strategic deferral in automobiles and steel, rule design leadership in digital trade, and endogenous accumulation in strategic supply chains. Empirical findings show that Japan has institutionalized a flexible coordination strategy through the alignment of the USJTA/USJDT, CPTPP and IPEF frameworks, and the Economic Security Promotion Act (2022) with subsidy and R&D instruments. However, structural constraints persist, including external dependence in semiconductor and critical mineral value chains, limited enforcement capacity in IPEF, U.S. recalibration of digital trade rules, and the inherent conditionality of autonomy under alliance asymmetry. The study argues that Japan’s post-2025 strategy requires reinforcing DFFT-based multi-layered rule coherence, advancing regional supply chain diversification, and strengthening absorptive, buffering, and innovation capacities under ESPA. Conceptually, the study reframes autonomy as conditional and structurally mediated, offering a comparative model for analyzing middle-power economic security trade strategies.