The effect of the surface elastic deformation is investigated by the multiscale approach in the hydrodynamic wedge-platform thrust bearing with the ultra low clearance on the 1nm scale, by incorporating both the non-continuum pure adsorbed layer flow and the multiscale “sandwich” film flow. The pure adsorbed layer flow in ultra small surface separations is described by the non-continuum nanoscale flow equation; The “sandwich” film flow is described by the multiscale flow equations respectively for the adsorbed layer flow and the intermediate continuum fluid flow. The numerical calculation results show that in the studied bearing, the effect of the surface elastic deformation is normally significant, it pronouncedly reduces the maximum film pressure, greatly changes both the film pressure profile and the surface separation profile, and considerably increases the minimum surface separation, which occurs on the exit of the bearing. The effect of the surface elastic deformation is shown to be obviously dependent on the fluid-bearing surface interaction.