Depth-resolved structure analysis of a polystyrene-b-poly(2-vinylpyridine) (S2VP) thin film (420 nm thick) was achieved by grazing-incidence small-angle X-ray scattering (GISAXS) utilizing low-energy X-rays ("tender" X-rays). In contrast to techniques utilizing hard X-rays, a gradual change of the penetration depth of soft X-rays around the critical angle of total reflection of a polymer surface is anticipated. In this research, X-ray energy of 2.4 keV was chosen to control the penetration depth and achieve depth-sensitive GISAXS measurement. Microphase-separated structure of the annealed S2VP in the thin film was confirmed to be hexagonally packed cylinders (HEX) aligned parallel to the substrate surface. Significant elongation of the Bragg spots in the q(z) direction was observed for an incidence angle close to the critical angle. The experimental full width at half-maximum (fwhm) values of the (11) HEX diffraction spot was interpreted using the theoretical fwhm values estimated using the Laue function considering an attenuation decay of X-ray intensity. The penetration depth was controlled by changing the incident angle, and depth-resolved structure analysis revealed that the hexagonal lattice deformed along the depth direction with the deformation gradually relaxed toward the surface. The observed relaxation behavior is related to the higher mobility of polymer chains near the surface.