Museums in Taiwan and Japan share close ties in terms of developmental processes, institutions and social environment. Beginning as early as the period of Japanese colonization of Taiwan (1895-1945), the prototype of Taiwan,s museums has continued to expand and evolve into the diversity and wide-ranging breadth of today. For the past century, national museums in both Taiwan and Japan have received a diversity of resources from their respective central governments and have become important social education institutions. With a focus on national museums, this paper discusses the changes in museum ecology in Japan and Taiwan. The scheme of“independent administrative institution”has been implemented in Japan for several years and has often been discussed in Taiwan. This study attempts to explore the pros and cons of implementation of this scheme in the Tokyo National Museum, in the context of special exhibitions, as well as to look for opportunities for future development and to predict difficulties, to serve as a reference for museums in both countries.