Brittle shallow crustal faults typically develop a complex fault zone architecture with distinct structural domains that display diverse microstructures, mineralogy, and deformation mechanisms. The development of such domains is typically controlled by the strength and composition of the protoliths, physical conditions of deformation, fluid ingress, and diachronous fault growth in response to stress accumulation and co-seismic slip. Herein, we studied the microstructure-mineralogy-kinematics of fault rocks in the Nahan Thrust, in the vicinity of the Main Frontal Thrust that represents a tectonically active zone in the Himalayan orogen. The Nahan Thrust is characterized by alternating red and gray gouge layers, and a single black gouge layer. Our results from electron microscopy and X-ray diffractometry indicate that the protolith of the red gouge layers is argillaceous sandstone, whereas that of the gray and black gouge layers is sandstone. Microstructures suggest an initially distributed deformation (aseismic creep), followed by a protracted brittle deformation event, and a later aseismic creep stage. The brittle stage is marked by progressive localization of stress, fracture development, cataclasis, frictional sliding, and seismic slips. The black gouge layer acted as the principal slip zone and exhibited ultrafine bands of micrometer-scale slip zones with vapor escape structures and clay clast aggregates, indicating seismic faulting and frictional heating during seismic slips. The preferential seismic rupture nucleation in the black gouge layer indicates a strong lithological dependence on seismic slip in the Nahan Thrust. We also conclude that heterogeneity within the Nahan Thrust resulted from primary lithological variations of the protoliths.