In the initial stage, the status quo of aquatic products industry in Taiwan and Zhoushan is analyzed. The aquatic products industry in Taiwan is characterized by high input, high output, advanced fishery import and export trade, refined and specialized fishery organizations and the dominant role played by the government. However, in Zhoushan, there are many problems in the development of aquatic products industry, featuring weak brand consciousness, inadequate famous brand and pillar industries, frequently restricted by green trade barrier and disordered competition of aquatic products market. The comparative advantages of aquatic products Cross-Straits are measured by using revealed comparative advantage index (RCA) and trade specialized index (TSC), the results show that the aquatic products in both the mainland and Taiwan have certain market share and competitiveness. The revealed comparative advantage index （RCA）of Taiwan’ aquatic products is higher than that in the mainland, while the RCA index in the mainland and Taiwan all shows descending trend; the trade specialized index(TSC) cross straits is positive, which indicates specialized export, but this specialization also shows descending trend. Taiwan has advanced aquaculture technology and the mainland owns cheap labor cost and low price, but due to the limited resources in the Taiwan Island and the backward processing technology of aquatic products in the mainland, the comparativeness of aquatic products in the mainland and Taiwan has slid slightly. Therefore, I probe into the cooperation modality between Zhoushan and Taiwan in terms of mutual investment in aquatic industry, exchange and training for personnel cross straits and establishing experimental point of aquatic industry of the Zhoushan Island and Taiwan Island. Besides, countermeasures for enhancing the international comparativeness of aquatic industry in Zhoushan Island are put forward.