Abstract: Fujian, as one of the four provinces included in the west coast economic zone, is relatively week in total economic output and scientific innovation, which limits Fujian′s leading role in promotion of science and technology cooperation.Therefore, it is critical for Fujian to fully utilize national supporting policies, excavate potential in cooperation with Taiwan, develop Fujian′s advantage and avoid the disadvantage, and study on more effective developing mechanism and policy in order to estimate the subject position in the science and technology cooperation of west coast economic zone of Taiwan Straits.