The essence of free trade zones lies in addressing development challenges through institutional opening-up and innovation-driven growth. Sustainable development constitutes the fundamental goal of free trade zone construction, opening-up and innovation serve as the core driving forces for their development, and a sound business environment acts as a critical guarantee for their efficient operation. Therefore, based on the panel data of 22 free trade zones in China from 2013 to 2022, this paper adopts Principal Component Analysis (PCA) and Analytic Hierarchy Process (AHP) to conduct a comprehensive evaluation of their sustainable development levels from six dimensions: environmental optimization, economic development, opening-up, radiation-driven capacity, business environment, and scientific and technological innovation. The results indicate that, first, the overall comprehensive scores of free trade zones in sustainable development show an upward trend with obvious regional divergence in growth rates. Coastal free trade zones maintain robust growth momentum, inland ones achieve steady progress, and border free trade zones witness modest growth. Second, the comprehensive scores of the 22 free trade zones in 2022 present a gradient distribution, reflecting prominent regional development imbalance. On this basis, targeted policy recommendations are put forward in this paper.