One prominent concept in Japan’s disaster response landscape is the Ecosystem-based Disaster Risk Reduction (Eco-DRR) strategy, widely acknowledged and applied in current disaster management practices. This paper systematically explores the foundational concepts of Eco-DRR and its evolution in the realm of disaster prevention and mitigation research in Japan. Local cases are cited to illustrate the implementation of Eco-DRR’s three major initiatives: suppressing the occurrence of hazardous natural phenomena, avoiding risk exposure, and reducing vulnerability. The study synthesizes the implementation structure and research trajectory of Eco-DRR in Japan’s disaster prevention, mitigation efforts, and ecosystem preservation, emphasizing the significance of traditional wisdom. In conclusion, the study advocates for the exploration and organization of traditional Eco-DRR wisdom in various regions, the integration of the Eco-DRR concept into policy frameworks with broad stakeholder participation, and a heightened focus on interdisciplinary exchanges in academic research.