Abstract: Over 27 years, the agricultural cooperation between Fujian and Taiwan has been fruitful by making better use of the resources of both sides. Meanwhile it is also facing strategic transformation under new circumstances. This article, adopting the approach of combining theoretical analysis and positive research, points out that modern high-tech agriculture has become the common goal of agricultural development of Fujian and Taiwan. In order to adapt to the requirements of promoting agricultural development of Fujian and Taiwan in modern times, the adjustment of common cooperation strategy is required so as to optimize resources and in the long run fulfill the win-win goal in a higher level.