The China’s Pilot Free Trade Zones (FTZS) are important carriers of greater openness and bear the burden of institutional innovation. Based on this, this paper empirically explores the economic effects caused by institutional innovation in pilot free trade zones from the perspective of factor flow and economic growth. It is found that the establishment of free trade zones has a significant promoting effect on the local GDP growth rate, the flow level of traditional factors and the flow level of innovative factors, and this conclusion is still valid after a series of robustness tests. Specifically, on the one hand, free trade zones in Shanghai, Guangdong and Fujian all significantly increased the local GDP growth rates, free trade zones in Guangdong, Fujian and Tianjin has significantly promoted the flow of traditional factors and innovative factors; on the other hand, the promoting effect of Fujian free trade zones on economic growth showed an inverted U-shaped trend over time, Tianjin Free Trade Zone on the GDP growth rate is not obvious, Shanghai Free Trade Zone only promoted the flow of innovative factors, but had no obvious effect on the flow of traditional factors.