Abstract: The establishment of Fujian Free Trade Zone builds a new platform for cross-strait trade exchange and industrial connection. It also provides new opportunities for the innovation of agricultural cooperation mechanism between Zhangzhou and Taiwan. The current situation and problems of agricultural cooperation between Zhangzhou and Taiwan were summarized and analyzed in this paper. Then, based on the analysis, a series of countermeasures were put forward including strengthening agricultural industrial connection, promoting the exchange and interaction of agricultural association, enhancing financial innovation and so on, thus to innovate the agricultural cooperation mechanism between Zhangzhou and Taiwan.