Temporal fault-zone observations are important to better understand the evolution of fault structure and stress configuration. However, long-term monitoring in the fault zone is rare after a large earthquake. Here, we use seismic data in the fault zone at 1-km depth from the Taiwan Chelungpu-fault Drilling Project to study long-term anisotropy after the 1999 Mw7.6 Chi-Chi earthquake. The direct S-wave splitting measurements resolve the overall weak anisotropy in the shallow crust. In order to resolve fault damage zone anisotropy, we perform coda cross-correlation technique for 794 microearthquakes between 2007 and 2013. We estimate the temporal change in background shear-wave velocity, fast shear-wave polarization direction (FSP), and strength of anisotropy (Aani) in the fault damage zone. We show the average FSP direction is N93°E with a significant Aani of about 12%, likely due to the pervasive vertical microcracks created after the earthquake. Temporal variations of anisotropy exhibit seasonal variation with periodicity every 9–12 months that correlates with rainfall events. Furthermore, long-term anisotropy shows a gradual rotation of FSP direction of about 15° during the first 4 years of observation. At the same time, the strength of anisotropy reduced from 17% to 10% and shear-wave velocity increased, suggesting the fault healed after the earthquake. This study reports in-situ evidence for two key observations: (a) long-term, fault-zone healing after a major earthquake and (b) modulation of 1-km deep fault-zone properties by surficial hydrologic processes. These observations may provide constraints on the response of the fault damage zone in the interseismic period.