Evolutionary history of Nojima Fault zone is clarified by comprehensive examinations of petrological, geophysical, and geochemical characterizations on a fault zone in deep‐drilled core penetrating the Nojima Fault. On the basis of the results, we reconstruct a whole depth profile of the architecture of the Nojima Fault and identify the primal slip layer activated by 1995 Kobe earthquake. The deepest part (8‐ to 12‐km depth) of the fault zone is composed of thin slip layers of pseudotachylite (5 to 10 mm thick each, 10 cm in total). Middle depth (4‐ to 8‐km depth) of the fault zone is composed of fault core (6 to 10 m thick), surrounded by thick (100 m thick) damage zone, characterized by zeolite precipitation. The shallow part of the fault zone (1‐ to 4‐km depth) is composed of distributed narrow shear zones, which are characterized by combination of thin (0.5 cm thick each, 10 cm in total) ultracataclasite layers at the core of shear zones, surrounded by thicker (1 to 3 m thick) damage zones associated with carbonate precipitation. An extremely thin ultracataclasite layer (7 mm thick), activated by the 1995 Kobe earthquake, is clearly identified from numerous past slip layers, overprinting one of the shear zones, as evidenced by conspicuous geological and geophysical anomalies. The Nojima Fault zone was 10 to 100 times thicker at middle depth than that of shallower and deeper depths. The thickening would be explained as a combination of physical and chemical effects as follows. (1) Thickening of “fault core” at middle depth would be attributed to normal stress dependence on thickness of the shear zone and (2) an extreme thickening of “damage zone” in middle depth of the crust would result from the weakening of the fault zone due to super hydrostatic fluid pressure at middle depths. The high fluid pressure would result from faster sealing with low‐temperature carbonate at the shallower fault zone.