Abstract:  Nowadays, with the advancement of the construction of pilot free trade zone, the trade market between Fujian and Taiwan has become more international, the exchange and cooperation of talents have become more frequent, and the prospect of cooperation on the cross-strait service trade has been broader.On the basis of analyzing the current situation of e-commerce development of agricultural products between Fujian and Taiwan, this paper considered that there were some problems existed, such as ineffective construction of e-commerce platform, the shortage of talents, imperfect logistics distribution system of agricultural products, etc.Therefore, a series of countermeasures for promoting the e-commerce development of agricultural products between Fujian and Taiwan were put forward, which included seizing the opportunity of construction of Fujian pilot free trade zone to improve the e-commerce platform of agricultural products by relying on cross-border e-commerce in pilot free trade zone, and to promote the cooperation of e-commerce talents of agricultural products by relying on cross-strait talent exchange, etc .