On the basis of the revealed comparative advantage index( RCA index) and the index of export growth advantage, this paper makes a systematic research of the effect of ECFAs signature and implementation on the related product competitiveness in the three major industries of Fujian Province. The research finds that after the implementation of ECFA, the competitiveness of most related products in the first and second industries has different degrees of improvement, whereas the overall trend of the third industry with relatively weak comparative advantage is bullish, although it is subject to certain impact. Therefore, in the post ECFA era, Fujian and Taiwan should, with the new green agriculture (fishery) industry, advanced manufacturing industry and modern service industry as the focus, strengthen industrial cooperation between Fujian and Taiwan, optimize the traditional industry in Fujian, construct the platform for the industrial cooperation between Fujian and Taiwan , promote two way investment docking,speed up the establishment of industrial division and cooperation and gain the mutual benefit of win win system.