The Taiwan Chelungpu-fault Drilling Project (TCDP) Hole-A recovered continuous core samples across the rupture zone of the 1999 Chi-Chi earthquake (Mw7.6). Studying in-situ chemical properties sequentially from fresh-fault-zone materials of the Chelungpu fault provides insight into possible faulting mechanisms. Distinct anomalies of mineral assemblages at the 1111-m fault zone of TCDP Hole-A are found to be: (1) A decrease in clay content within the primary slip zone (PSZ); and (2) A significant decline of illite, disappearance of chlorite and kaolinite, and spike in smectite within the PSZ. Meanwhile, features relating to melting or amorphous material in the PSZ have been observed by SEM and TEM. The results suggest that the PSZ might have experienced generation of glassy materials such as pseudotachylyte by the expense of clay minerals due to strong shear heating, then prompt alteration of pseudotachylyte into smectite. Characteristics of clay minerals and images obtained from electronic microscopes in the PSZ thus imply that pseudotachylyte possibly developed during the 1999 Chi-Chi earthquake, but quickly altered into smectite. This particular phenomenon may explain why pseudotachylyte is rarely found in exhumed hydrated fault zones.