Abstract: Fujian Province possesses special geographical location and a long culture history, which makes it the frontier area and important platform for exchange and cooperation of economy, culture between mainland China and Taiwan. In this study, the current situation and existing problems of economic and trade cooperation between Fujian and Taiwan were analyzed, and the favorable influences and opportunities produced by the construction of free trade zone were summarized. Then, three suggestions for deeper economic and trade cooperation between Fujian and Taiwan were put forward, including innovating supervision and management environment of trade to promote the development of free trade; expanding financial cooperation and improving financial opening; facilitating free flow of personnel in the free trade zone.