Abstract:  Fujian is the first region of Taiwan economy and trade, it has a good foundation in financial cooperation between Fujian and Taiwan. The official signature of ECFA offers the opportunities and platform for establishing financial institutions mutually, deepening capital market cooperation and building crossstrait regional financial service center. Now, the financial cooperation between Fujian and Taiwan has obtained the plenteous results. But the challenges come after the opportunities, after entering the ECFA era, the financial cooperation between Fujian and Taiwan also faces challenges such as the enhancement of regional competition, the increase of difficulty of financial supervision, the faultiness of complete currency settlement mechanism. Therefore, Fujian must take the establishment of the crossstrait regional financial centre as an emphasis to deepen financial cooperation between Fujian and Taiwan and promote the mutual development of the two regions through the paths such as strengthening industrial connection, talent exchange, establishing offshore financial center．