•Pilot Free Trade Zones (PFTZ) can promote green technology innovation efficiency.•Providing reference for developing countries to develop green economy.•Proposing a more holistic index system of green technology innovation efficiency.•The impact of PFTZ exhibits significant spatial heterogeneity.•Market potential affects the green effect of PFTZ. The Pilot Free Trade Zone (PFTZ) policy represents a significant step in China’s institutional innovation and broader opening-up, crucial for fostering green and high-quality economic growth. The existing literature has conducted in-depth studies on the economic effects, energy conservation, emission reduction and green innovation of PFTZs, but the effect on green technology innovation efficiency (GTIE) remains underexplored. Institutional innovation in the PFTZs will profoundly affect regional green development, and green innovation, and will certainly affect the regional GTIE. Based on this, this paper uses the city-level data of prefecture-level cities in China from 2005 to 2020 to empirically test the impact of PFTZ establishment on GTIE. First, the Super-SBM model was applied to evaluate the GTIE across 281 Chinese cities. Then, taking the establishment of PFTZs as a quasi-natural experiment, the multi-stage differentially differential model is constructed to empirically assess PFTZ policy’s impact on GTIE. The findings indicate that PFTZs can significantly enhance the GTIE. This improvement is facilitated through four pathways: the digital economy, the high-tech industries agglomeration, innovation agglomeration, and talent agglomeration. The results offer strategies for balancing external openness with environmental protection in developing countries and furnish empirical support for creating high-quality development frameworks.