Abstract: By using the method of SWOT analysis, the strength, weakness, opportunity and threat of the economic and trade cooperation between Fujian and Taiwan were analyzed. And the data before and after the signing of Economic Cooperation Framework Agreement were compared. The result showed that ECFA has beneficial effects on the import and export, mutual investment, and industrial cooperation between two sides. However, some problems such as one-way benefit from Fujian, import and export growth unstably, ability to attract investment decreased and industrial structure optimization in cooperation haven’t been solved. Therefore, Fujian should enhance the competitiveness of export products, improve the investment environment, build Pingtan experimentation area, optimize the industrial structure to deepen the economic and trade cooperation between Fujian and Taiwan.