With regard to polyesters based on biobased 2,5-furandicarboxylic acid (FDCA), our work presents a new strategy, heteroatom substitution, to adjust the thermal and gas barrier properties. The effects of nonhydroxyl oxygen heteroatoms in the diols on the properties of FDCA-based polyesters were first investigated by a combination of an experiment and molecular simulation. The results demonstrated that the introduction of oxygen heteroatoms significantly influenced the thermal and gas barrier properties. As for the two model polymers with a very similar skeleton structure, poly(pentylene 2,5-furandicarboxylate) (PPeF) and poly(diethylene glycol 2,5-furandicarboxylate) (PDEF), their Tg exhibited an obviously increasing order. Moreover, they showed similar thermal stability and thermal oxidative stability. Dynamic mechanical analysis, positron annihilation lifetime spectroscopy, and molecular dynamics simulation indicated that the gas barrier properties followed the sequence of PDEF > PPeF mainly due to the decreased chain mobility and smaller fractional free volume. In-depth analysis of the effects of heteroatom substitution has an important directive significance for the design and preparation of new high glass transition temperature or novel excellent gas barrier materials. Through the manipulation of different heteroatoms in the diols, the polyesters with varied properties can be expected.