The aim of this paper is to extend knowledge on biobased poly(butylene furanoate)–block–poly (ethylene oxide) (PBF-b-PEO) copolymers’ performance by studying the effect of the PEO segment’s molecular weight on the microstructure and materials behavior. As crystallization ability of PEO depends on its molecular weight, the idea was to use two PEO segment lengths, expecting that the longer one would be able to crystallize affecting the phase separation in copolymers, thus affecting their mechanical performance, including elasticity. Two series of PBF-block-PEOs with the PEO segments of 1000 and 2000 g/mol and different PBF/PEO segment ratios were synthesized by polycondensation in melt, injection molded to confirm their processability, and subjected to characterization by NMR, FTIR, DSC, DMTA, WAXS, TGA, and mechanical parameters. Indeed, the PEO2000 segment not only supported the crystallization of the PBF segments in copolymers, but at contents at least 50 wt % is getting crystallizable in the low temperature range, which results in the microstructure development and affects the mechanical properties. While the improvement in the phase separation slightly reduces the copolymers’ ability to deformation, it is beneficial for the elastic recovery of the materials. The investigations were performed on the injection molded samples reflecting the macroscopic properties of the bulk materials.