Postseismic geodetic observations provide valuable constraints for inverting the mantle’s viscoelastic structure. The 2011 Mw 9.0 Tohoku-Oki earthquake in Japan generated remarkable coseismic and postseismic deformation, both on land and at the seafloor. Previous studies have exploited terrestrial GNSS data from various postseismic periods to investigate the viscoelastic structure near the epicentral region, capitalizing on their high accuracy and temporal resolution. In this study, we incorporated over a decade of GNSS-A (GNSS-Acoustic Seafloor Positioning System) observations from stations distributed along the subduction zone. The seafloor mechanical behavior was modeled as a Burgers viscoelastic material, and the layered viscoelastic structure beneath the subduction zone was inferred using half-space layered dislocation theory. We first derived the postseismic seafloor deformation signal by extracting decadal-scale displacement time series with preseismic trends removed. Then, leveraging the contrasting temporal behaviors of rapid afterslip decay and gradually dominating viscoelastic relaxation, we inverted for the Earth’s layered viscoelastic structure. The inversion incorporated radially stratified viscosity parameters of the seafloor and half-space layered dislocation theory, constrained by postseismic deformation observations from 3 to 9.5 years after the earthquake and implemented through a least squares framework. Results indicate that the root mean square (RMS) error remains relatively small and stable when the seafloor elastic thickness varies between 28 and 40 km, with minimal differences across this range. The minimum RMS of 6.81 cm corresponds to an optimal elastic thickness of 37 km.