Abstract:  Since the implementation of the strategy of the free trade zone, the strategic function of Fujian Free Trade Zone is mainly to take the advantage of Taiwan nearby, to promote the liberalization of investment and trade with Taiwan, and to establish crossstrait economic cooperation demonstration zone. The strategies promoting the economic and trade integration between Fujian and Taiwan in the construction process of Free Trade Area were discussed in this paper based on the regional comparison on economic and trade cooperation of Fujian, Guangdong, Jiangsu, Zhejiang and Shanghai, and the SWOT analysis on economic and trade integration between Fujian and Taiwan in the construction of Free Trade Area.