2,5‐furandicarboxylic acid (FDCA), a bio‐based monomer, was taken as a sustainable alternative to isophthalic acid (IPA) for the modification of poly(ethylene terephthalate) (PET). Results showed that FDCA was more effective than IPA in terms of reducing the crystallization activity of PET, because FDCA is more rigid and highly polar, which will hinder the PET chain packing during crystallization process. Moreover, modification of PET with FDCA resulted in copolyester with higher glass transition temperature, higher tensile modulus, better optical clarity, and gas barrier property, compared to those of IPA. With the addition of 20 mol % FDCA, the resulted copolyester poly(ethylene 2,5‐furandicarboxylate‐co‐ethylene terephthalate) (PEFT 20) was able to keep high transparency even after being annealed at 110 °C for 40 min. However, when 20 mol % of IPA was added, poly(ethylene isophthalate‐co‐ethylene terephthalate) (PEIT20) easily turned opaque under the same heat treatment. Therefore, less amount of FDCA was required in order to obtain the PET copolyester with better performance. The result indicated that FDCA had great potential to substitute IPA for the modification of PET from the point of view of industrial application. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47186.