This study examines the evolution of the center–periphery structure in Japanese intellectual history through the thought of Motoori Norinaga and Yanagita Kunio. It explores how Japan sought self-identity and independence under external cultural and academic pressures. During the Edo period, under the influence of Chinese civilization, Motoori Norinaga reinterpreted the Huayi distinction, emphasizing indigenous tradition and Shinto thought while rejecting China’s absolute centrality and repositioning Japan as a cultural center. In the modern era, facing a Western-dominated academic system, Yanagita Kunio proposed “national folklore studies” to secure the autonomy of Japanese scholarship through a strategy of relative centralization. By comparing their approaches, this study reveals both continuity and transformation in Japan’s center–periphery structure. It argues that despite differences in historical context and disciplinary focus, both thinkers retained the hierarchical logic of the center–periphery framework while redefining Japan’s position within it.