Abstract: Purpose/Significance Free Trade Zone (FTZ), an important basis for high-quality development, is a reform attempt under specific policy and location conditions. However, along with the new model is the emergence of new challenges and specific difficulties, thus bringing about the thinking of FTZ’s innovation quality. Design/Methodology Taking Fujian FTZ as an example, this paper adopts the improved entropy method to empirically test the FTZ’s innovation-driven development quality. Some insufficiencies are discovered in the talent mechanism, innovation input, regional exchange and market access, and some space for development can be found in formulating innovation standards and summarizing laws. Findings/Conclusions FTZs in China, as a key area of comprehensive reform experiment, should continue to improve the innovation ability, increase property investment and technical input, regard innovation as the industry screening criteria, expand exchanges between FTZs, draw on strengths of each other, and optimize the innovation environment, in a bid to accelerate the innovation progress of FTZs in the new era.