The present work is initiated to study the history perspectives of marine affairs and the organization structure of government for dealing with the ocean matter in Taiwan. According to neo-institutionalism approach, the ocean affairs must be managed and manipulated by the followed aspects: the international spirits and practices, the history of Taiwan ocean affairs, and the human rational actions. The international spirits and practices should be based upon with the current ocean governance, Agenda 21, United Nations Convention on the Law of the Sea (UNCLOS), and marine policies of major nations. These should be adapted into the bases of Taiwan ocean policies. Taiwan has long neglect overlooked the ocean by ignoring territorial waters, it has only with slogan of ocean country for the time being. The government has not made the clear responsibilities of ocean affairs among within the departments. Up to now it is still the Council of Ocean Affairs which will be established till 2012. Considering the rational choice, the establishment and transformation is still the hardest challenge for the management of ocean affairs. This thesis concludes that it would be best interest for the government to integrate the management spirit of marine affairs with international practice, because the affairs of surrounding ocean are increasingly complex. The current draft organization structure on the Council of Ocean Affairs could not easy to deal with sophisticated ocean affairs. Therefore, the Council of Ocean Affairs should be shaped to getting more dominant power instead of coordination power. The Department of Ocean is needed to handle the marine affairs instead of the Council of Ocean Affairs. Finally, extensive funding for affiliation and training human resource related to the establishment of the Council of Ocean Affairs will be beneficial to the ocean governance.