In early 2017, our country formed “1+3+7”web format free trade area development pattern. In 2017 October, the 19th National Congress of the Communist Party of China, Our country put forward further reform goal, and give free trade area even greater right of reform’ autonomy to explore the construction of free trade port. However, in the process of building the system of commercial registration, Free trade area appear such situation as normative documents more and legal registration less, commercial registration measures more and innovation system less ect., These system of commercial registration problems cannot crack in the system level. They maybe become system obstacle of the free trade area developing to free trade port. Therefore, we analyze the cause of current situation of free trade area commercial registration system, and propose the macro legislation of commercial registration of the free trade area at national level in order to make free trade area in our country legal system of commercial registration system to form resultant force, and avoid commercial registration system for regional innovation blindly to go toward the bottom of the competition. At the same time, we need to reconstruct commercial registration, and make private law autonomy as a starting point, further weaken government’s administrative functions in the process of commercial registration, make the commercial registration system for the international standards, we should make innovation and breakthrough in commercial registration system, and promote the rapid development of free trade experimental zone to the free trade port.