Since 2022, facing the challenges from declining R&D capability index, escalating geopolitical tensions, and the disruptive leap of emerging technologies, Japan gradually reforms its S&T systems under the blueprint “crisis driven, security bound, application oriented, capability rooted”. At the national level, the creation of the “Key and Advanced Technology R&D through Cross Community Collaboration Program” (K-program) and the AI Safety Institute marks the first time innovation policy has been tightly fused with comprehensive national security, while other important reforms—front-loading commercialisation, rebuilding the innovation ecosystem, and optimizing the research environment—bridge the traditional science-to-economy gap. At the institutional level, RIKEN and AIST serve as flagship models, by adopting matrix-style research organisations, “data + AI” paradigm, full-chain industry–university–institute start-up connect, and rigid research-security governance to strengthen their ability to deliver governmental missions. The reform measures on one hand address the current crises over R&D investment, talent, and security, while on the other hand seeking to secure future frontiers, revitalize industries, and sharpen competitiveness.