The construction of pilot free trade zones is an important initiative for China to deepen reform and opening up，and also a key link to realize green development. This article first introduces the connotation of green development and the environmental effects of the construction of pilot free trade zones，and then analyzes the theoretical mechanism of realizing green development in the pilot free trade zones，that is，the construction of the pilot free trade zones promotes green development mainly through the promotion of technological innovation，the optimization of the industrial structure and the improvement of the efficiency of resource allocation. On this basis，it reveals the challenges faced by China’s pilot free trade zones in realizing green development from five aspects，including ecological environment regulatory system，industrial green transformation tasks，green trade development level，green financial service quality，and green logistics facilities development. Finally，combining the theoretical mechanism analysis and practical challenges，this article proposes that China should promote the realization of green development in the pilot free trade zones by benchmarking the international high-standard economic and trade rules，developing strategic emerging industries，deepening the reform of the green trade system and mechanism，unblocking green financing channels，and sounding the green and low-carbon logistic system，so that green will become the eye-catching “bottom color” of the pilot free trade zones at an early date.