Neglecting fault segmentation in hazard assessments leads to underestimated potential hazard. Moreover, integrating the temporal evolution of fault segments activations in hazard assessment improve scenario’s reliability. In this view, enhanced seismic catalogs have potential in revealing previously neglected fault complexities. Past efforts were restricted to the 2D view analysis without involving the segment temporal activation. Our work provides a comprehensive approach, reconstructing 3D fault fine-scale geometry and segments activation evolution. We analyzed the 2014 Northern Nagano (Japan) (Mw 6.2) earthquake sequence using high-resolution seismic catalogs. We automatically detected and located about 2500 events between October and December 2014. We refined the automatic picks, based on cross-correlation and hierarchical clustering, and we relocated the hypocenters with the double-difference in 3D velocity models optimized for the area. Moreover, we calculated the composite focal mechanisms of the main clusters, crucial to constrain the 3D geometry of the fault segments, and rupture directivity that we interpreted jointly with the seismicity and the fault slip. We found that the multi-segmented fault system, is comprised of, at least, 9 distinct segments, that ruptured during 3 successive phases. Different segments exhibit a different rupture mechanism based on their spatial and temporal occurrence, influencing seismicity evolution and rupture length. The presented analysis can be used to improve the reliability of probabilistic hazard assessment in the high seismic potential area of the Itoigawa-Shizuoka fault system. The possibility of fault segment interaction and mutual triggering processes should be considered when drawing reliable seismic hazard scenarios.