Abstract: The agricultural scientific and technological cooperation is an important path of the agricultural sustainable development between Fujian and Taiwan. The research status of the agricultural scientific and technological cooperation between Fujian and Taiwan was summarized in this paper. And by using the theory of collaborative innovation mechanism, the“five-in-one” cooperation model involving the government departments, business organizations, universities, scientific research institutions and farmers was established. In addition, the general idea on the collaborative innovation mechanism of the agricultural science and technology between Fujian and Taiwan was put forward from the aspects of resource integration, major function localization, innovative element management, etc.