Pilot free trade zones, as an important measure under the requirement of China’s promotion of system-based opening in the new era, play an important role in promoting the coordinated development of regional economies. The article examines the impact of the pilot free trade zone policy on the coordinated development of regional economy using spatial econometric modeling with data from 30 provinces in China from 2013 to 2022. The study finds that the construction of the pilot free trade zones has effectively enhanced the coordinated development of regional economies; moreover, the establishment of the pilot free trade zones has promoted the level of coordinated regional economic development by enhancing the quality of trade, boosting social investment, and stimulating the vitality of innovation; Through further analysis, it is found that the impact of the construction of free trade zones on the coordinated development of the regional economy has a significant spatial spillover effect, and in the future, China should steadily expand the system-type opening up, unswervingly push forward the construction of the free trade zones, strengthen the cooperation and linkage of the construction of inter-regional free trade zones, and appropriately deal with the relationship between the market and the government, in order to push the results of the institutional innovations of the pilot free trade zones to be translated into the coordinated development of the regional economy The results of the Pilot Free Trade Zone system innovations will be transformed into coordinated regional economic development.