Two poly(hexamethylene 2,5-furandicarboxylate)-b-poly(diethylene glycol 2,5-furandicarboxylate) multiblock copolyesters were synthesized using two hydroxyl-terminated poly(hexamethylene 2,5-furandicarboxylate) (PHF-diol) and poly(diethylene glycol 2,5-furandicarboxylate) (PDEGF-diol) prepolymers in the presence of a chain extender hexamethylene diisocyanate. A series of techniques were employed to fully characterize the thermal, mechanical, and crystallization properties of the obtained multiblock copolyesters. 1H NMR results confirmed the expected multiblock structures. The combination of the two segments significantly improved the elongation at break of PHF without sacrificing the tensile strength. Moreover, the melt crystallization temperatures and melt points of the multiblock copolyesters only slightly decreased, due to the excellent crystallizability of the PHF segment. In addition, the PDEGF segment significantly influenced the tensile strength and hydrophilicity by forming hydrogen bonds between the adjacent molecular chains.