Temporal changes of seismic velocity and anisotropy in the shallow crust are quantified using local earthquakes recorded at a 200-m-deep borehole station CHY in Taiwan. This station is located directly above the hypocenter of the 10/22/1999, M6.4 Chia-Yi earthquake. Three-component seismograms recorded at this station show clear direct (up-going) and surface-reflected (down-going) P- and S-waves, and S-wave splitting signals. The two-way travel times in the top 200 m is obtained by measuring the time delays between the up-going and down-going waves in the auto-correlation function. The S-wave travel times measured in two horizontal components increase by ~1-2% at the time of Chia-Yi main shock, and followed by a logarithmic recovery, while the temporal changes of S-wave splitting and P-wave are less than 1% and are not statistically significant. We obtain similar results by grouping earthquakes into clusters according to their locations and waveform similarities. This suggests that the observed temporal changes are not very sensitive to the seismic ray path below CHY, but are mostly controlled by the variation of material property in the top 200 m of the crust. We propose that strong ground motions of the Chia-Yi main shock cause transient openings of fluid-filled microcracks and increases the porosity in the near-surface layers, followed by a relatively long healing process. Because we observe no clear changes in the shear wave anisotropy, we infer that the co-seismic damages do not have a preferred orientation. Our results also show a gradual increase of time delays for both the fast and slow S-waves in the previous 7 years before the Chia-Yi main shock. Such changes might be caused by variations of water table, sediment packing or other surficial processes.