Applying deconvolution interferometry technique to surface‐borehole (down to 300 m) seismogram pairs of KiK‐net, we retrieved temporal changes in S wave velocities and polarization anisotropies associated with the 2016 Kumamoto earthquakes, Japan. The average S wave velocity decreased after the largest foreshock (Mw 6.2) and again after the Mw 7.0 mainshock, in the latter case, by as much as 6.4%. The seismic velocity susceptibility (SVS), defined as the ratio of the relative S wave velocity change to the maximum dynamic strain, ranged from −170 to −13. The absolute value of the SVS was larger at the sites near the ocean or covered by an embankment. Systematic changes were not observed for SVSs obtained after the largest foreshock and mainshock. At most sites, the average S wave velocity continued to recover for at least 1 year, proportional to the logarithm of the lapse time after the mainshock. The speed of the log‐time recovery (m‐value) appears to be independent of the maximum dynamic strain of the mainshock. Large m values were observed at the sites of large absolute SVS values, indicating that a more susceptible medium is more resilient. The strength of the S wave polarization anisotropy (anisotropy coefficient) increased by up to 0.8% after the mainshock, which was much smaller than the relative change in the average S wave velocity and was below the background change due to phenomena other than earthquakes. These observations can be explained qualitatively by considering fracture theory in a medium that contains many vertical cracks with randomly oriented polarizations.