Abstract: Currently, ecological agriculture has become an important way to achieve sustainable development of agriculture in China. With the continuous deepening of ecoagricultural cooperation between Fujian and Taiwan, it has been transiting from “resource integration” to “synergic development”, and also has its realistic feasibility. Therefore, it is thought that the basic idea should be based on achieving the knowledge appreciation as the core, and use the two dimensions of integration and interaction to promote the deep integration of production, teaching and research by following the process of full communication-coordination with each other-mutual cooperation-comprehensive collaboration in an orderly manner. Then, the countermeasures for building self-organizing coalition are put forward from the angles of government, enterprises, universities and research institutions respectively, thus to achieve the mutual beneficial and win-win cooperation of ecological agriculture between Fujian and Taiwan.