Besides public exhibition, there is a group of scientists that carry out scientific research in the museum. There are two research buildings and a marine station in the museum, dedicated to the research in marine biology and ecology, aquaculture, propagation and conservation of marine fauna and flora.

　In 1997, the museum also provides help to other governmental divisions in dealing with endangered or threatened aquatic animals, and the rescue of grounded dolphins and whales. This is the largest marine biology research unit in Taiwan, working together with other universities and research institutes both in Taiwan and worldwide through joint programs.

　The joint establishment of two institutes with National Dong Hwa University in 2005, the Institute of Marine Biodiversity and Evolution, and Institute of Marine Biotechnology, is to enhance the development of marine sciences and biotechnology, and nurture the talented persons in those fields. The “Innovation Incubation Center” created in 2006 further advances us to the business world of international marine biotechnology and provides us with further opportunity in the area.