Mie Prefecture, Japan, and Taiwan signed an “MOU of Industrial Cooperation” in July, 2012. Based upon a triangle linkage of industrial, governmental and academic sectors in Mie Prefecture coupled with the strong policy support, the two parties have had a successful industrial, tourist and academic exchanges and cooperation for the past two years. It has served as a good example for Japan and Taiwan to promote a regional industrial cooperation with other areas. This paper first explores the background of why Mie Prefecture started Japan-Taiwan industrial alliance and then discusses the present situation and the characteristics of the Industrial cooperation between Mie Prefecture and Taiwan. It also analyses the result of the questionnaires regarding the view-points of corporations in Mie Prefecture about Japan-Taiwan industrial alliance. The result of the research has made clear that even though currently there are not many cases of industrial cooperation between Mie Prefecture and Taiwan, because of the short experimental period of two years, it is definitely worth watching, and that this particular case will serve as an importance reference for cross-border industrial cooperation.