A new bio-based copolyesters, poly(ethylene 2,5-furandicarboxylate-co-ε-caprolactone) (PEFCL), were synthesized from 2,5-furandicarboxylic acid, ethylene glycol and ε-caprolactone. The obtained copolyesters were characterized in terms of chemical structures, thermal and mechanical properties. The characterization results of 1H NMR and 13C NMR had confirmed the insertion of lactones units in PEF chains, all PEFCL copolyesters showed random microstructures. These bio-based copolymers were amorphous and had one glass transition temperature decreased as increasing the CL content. The thermal stability of PEFCL is slightly lower than PEF. Tensile testing revealed that introduction of ε-caprolactone into PEF chains impart PEFCL with excellent mechanical performance, typically, PEFCL40 had a Young’s modulus 1182 ± 80 MPa, a tensile strength 51 ± 3 MPa and an elongation as high as 981 ± 117%.