Thermoplastic poly(ether-ester-urethane)s were synthesized from poly(L-lactide) diols (PLLA diols), polytetrahydrofuran diol (PTMG diols), 4,4′-dicyclohexylmethane diisocyanate (HMDI), and 1,4-butanediol (BDO) by a two-step reaction, and the morphology and property of the resultant TPU could be adjusted by varying the PLLA contents. The soft segment was composed of PLLA and PTMG diols. By controlling the percentage of PLLA in the soft segment, the glass transition temperature and mechanical properties of the polyurethanes could be regulated. Based on the FTIR spectrum, we found that two kinds of hydrogen bonding existed individually in soft matrix and hard domain. The hydrogen bonding in soft matrix was unstable, which could be destroyed during elongation. With in situ stretching WAXS and SAXS experiments, we found that the PLLA crystal was destroyed and the PLLA domain oriented along the stretch direction. Finally, we proposed a schematic model to illustrate the microstructures of these elastomers before and after stretch.