The importance of maritime affairs is increased gradually in international society, and we should adjust the traditional thinking mode of ”emphasizing land and ignoring ocean”, focusing on the prospective issues of maritime affairs and agency. This article applied the research methods of articles review, content analysis and in-depth interview, distinguished maritime affairs agency in Taiwan into three periods of pre-integrated, post-integrated and under new Executive Yuan framework, and discussion the characteristics and predicaments in each period. And then depending on the theory of organizational change, this article examined the organizational change features in each period from three dimensions including the main driven-force of change, the speed of change and the scope of change. This article points out that the performance of maritime affairs agency change depends on the adoption of effective organizational change strategy to resolve the puzzles of organizational reengineering process.