The influence of water absorption on molecular dynamics, microstructures and relaxation behaviors of polyurethane (PU) elastomers with polyether (poly(tetramethylene glycol), PTMG) soft segments has been studied. Kinetics of water absorption of PU elastomer can be well fitted by Fick's model. However, non-Fickian absorption behavior was observed in the late stage at 60 °C, which was presumed to be related to the plasticization of some hard domains. Broadband dielectric relaxation spectroscopy was used to investigate the molecular dynamics of PU elastomers. The analysis of α-relaxation and Maxwell-Wagner-Sillars interfacial polarization indicated that the water absorption has a great influence on the molecular mobility of soft segment and the interface regions between soft domains and hard domains. Microphase separation structures of PU elastomers consisted of loose, partially regular and compact hard domains. Water molecules could interact with loose hard domains and lead to the plasticization. The results of stress relaxation behavior indicated that water absorption leaded to remarkable increase in the stress relaxation ratio. The deterioration of relaxation properties caused by water absorption was not only related to the soft segments, but also caused by the plasticization of the interface regions and the hard domains.