Abstract: 【Objective/Meaning】It is of great significance for the development of Fujian free trade zone to analyze its effects on the import and export of agricultural products between Fujian and Taiwan and propose corresponding suggestions for the construction of Fujian free trade zone.【Methods/Procedures】In this article, we firstly introduced the basic situations of Fujian free trade zone construction, and elaborated the recent conditions and problems for the import and export of agricultural products between Fujian and Taiwan.Then the changes of agricultural import and export between two provinces before and after Fujian free trade zone establishment were comparatively analyzed to determine the influence of free trade zone on agricultural trade.【Results/Conclusions】For the development of Fujian free trade zone, it was suggested to construct logistics system between Fujian and Taiwan, to enhance the administrative management team, to accelerate the transformation of government functions, and to pay enough attention on the construction of cross-border e-commerce platform.