This article briefly analyzes the development status of China (Chongqing) Pilot Free Trade Zone and Chongqing Port Logistics firstly, and then, the mechanism of interaction between the free trade zone economy and the logistics development of Chongqing Port is discussed from a qualitative perspective. Finally, according to the development status of Chongqing Port Logistics, some countermeasures are put forward to solve its development problems and realize the benign interaction between the free trade zone economy and Chongqing Port Logistics.