In 1987, Dr. Zhang KuenXiong, who then worked in Institute of Zoology , Academia Sinica, was delegated by the Council to direct the project. He was expected to highlight the cultural particularity and regional ocean resources in PengHu by making best use of people's understanding about the ocean as well as about the historical development of ocean. Moreover, it was also a task upon him to offer an interpretation for future direction of ocean development, and to collect, arrange, and display materials of ocean-specific in a systematic way from the perspective of humanism and natural science.

In April, 1988, the project was approved by Council for Cultural Affairs. The same year in June, a supervising committee was established. The funds for the project came respectively from Council for Cultural Affairs of 6 millions, Provincial Education Hall of 5 millions, PengHu County of 2 millions, and made a total of 13 millions dollars.

In April, 1993, JunHan Design Company was appointed to design the construction of the museum. In March, 1994, after the design was completed, the construction project was started. Then HunGe Advertising Decoration Company won the bid and started the construction. It was completed in October, 1994. The same year on Christmas Eve, the museum was opened.