In order to promote the construction of free trade zone and the innovation of system and mechanism, this paper puts forward the application research of big data intelligent management technology in the construction and innovation of free trade zone. By analyzing the implementation methods and steps of big data technology in the logistics management of Free Trade Zone A, this paper puts forward some ways to improve the logistics management system of Free Trade Zone, including building a big data logistics platform, improving operational capacity and forming agglomeration advantages. It is hoped that it can provide some basis for the mechanism innovation and economic and social development of FTZ, enhance China's ability of social, economic and environmental sustainable development, and realize the urgent need of sound and rapid economic development, and help FTZ embark on a brand-new development path. Taking the construction of free trade zone as an opportunity to promote the innovation of system and mechanism will be based on the transformation of government functions, so that the intelligent equipment manufacturing industry and the producer service industry will continue to integrate and create a new supply of government investment and management models.