The establishment of the China Pilot Free Trade Zone complies with the concept of sustainable development, and its construction can not only realize trade liberalization and facilitation but also activate the green innovation momentum of enterprises to help solve China's current dilemma of sustainable development and economic growth. This paper is the first to consider the impact of the establishment of the pilot free trade zone from the perspective of enterprise green innovation efficiency, providing a direct answer to the key question of whether the construction of the pilot free trade zone can truly serve the high-quality development of the economy in the new era, and enriching the theoretical research on the enterprise green innovation efficiency macro-drivers related theoretical research. In addition, this paper uses the super-efficient EBM-GML model to measure the level of green innovation efficiency of enterprises, on the basis of this, it adopts the multi-stage differences-in-differences method used to evaluate the impact of the establishment of the pilot free trade zone on the green innovation efficiency of enterprises. According to the benchmark regression results, the establishment of the pilot free trade zone has promoted the degree of green innovation efficiency of enterprises, and this promotion effect is sustainable. This conclusion was validated by robustness tests. Heterogeneity testing confirms that the pilot free trade zone has a significant influence on the green innovation efficiency of enterprises in heavy pollution industries, non-state-owned enterprises and patent-intensive enterprises. With the enhancement of environmental regulations, the green innovation efficiency of enterprises shows significant improvements. The analysis of the transmission mechanism shows that the pilot free trade zone influences the green innovation efficiency of enterprises primarily through the cost reduction effect, tax incentive effect, and reverse technology spillover effect. This study clarifies whether the policy of the pilot free trade zone can boost the green innovation efficiency of enterprises, and provides useful insight for further implementing the strategy of opening up to the world and promoting high-quality economic growth.