The establishment of China Pilot Free Trade Zones is an important measure for China to push ahead with the new round of reform and opening up. Chongqing and Shanghai Pilot FTZ have common characteristics in objectives, positioning and tasks, but compared with the Shanghai Pilot FTZ, Chongqing Pilot FTZ has obvious heterogeneity in the operating basis, endowment conditions and functional orientation. The innovative development of Shanghai Free Trade Zone highlights global, overall, comprehensive and leading character but Chongqing Free Trade Zone emphasizes regional and functional character. Although the construction basis of Chongqing Free Trade Zone is weaker than that of Shanghai Free Trade Zone, Chongqing Free Trade Zone takes the advanced position of the upriver connection point of “One Belt and Road” and has the advantage of railway port. Chongqing Free Trade Zone should learn and popularize the advanced experience of Shanghai Free Trade zone, sufficiently bring self advantages into fully play, learn from both domestic and foreign experience, promote factors free flowing by going to visit other free trade zones and to introduce new equipments and ideas, actively explore new regulations of land trade, deepen financial reform and opening-up in order to make contributions to overall deepening reform and opening-up and promoting the development in the western regions.