Abstract: The implementation of the two strategic policies of Fujian Pilot Free Trade Zone and the 21st Century Maritime Silk Road has brought an unprecedented endogenous power and a great opportunity for the transformation and upgrading of Fujian’s regional economies. Now it has become an important task for Fujian to seize the development opportunity. Based on this background, the advantages, disadvantages, development opportunities and challenges faced by Fujian FTZ in constructing the core area of the 21st Century Maritime Silk Road were analyzed in this paper. Then, the innovation development path for Fujian to promote and improve the new system of open economy which relied on the trade liberalization was explored from the six aspects of innovating the cross-strait cooperation mechanism, creating a new all-dimensional opening-up pattern of Fujian FTZ, optimizing the investment environment in Fujian Province, stimulating the leading and demonstrating effect of Fujian FTZ, promoting the transformation and upgrading of the traditional leading industries and optimizing the industrial structures.