The structural dynamics of pure niobium (Nb) contacts with a width of several nanometers (nanocontacts (NCs)) during the energization using nanosecond pulse-width voltages was observed in situ by transmission electron microscopy. The conductance of Nb NCs was simultaneously measured. As pulse waves with 4 ns width and 0.88 V in average height were impressed to crystal-state Nb NCs, phase transformation into amorphous states was observed. Subsequently, average pulse-width voltages lower than that of the amorphization voltage, i.e., 0.32 V, were impressed to amorphous state NCs, resulting in the inverse phase transformation, i.e., crystallization. In particular, the impression of the lower pulse-width voltages caused stepwise crystallization in the amorphous state NCs, corresponding to multiple stepwise conductance variations. The step height in the stepwise conductance variation depended on the external shape of NCs, the injected energy, and the stage of the stepwise crystallization. This stepwise conductance variation leads to the applications of Nb NCs to optimized ultimate fine multi-level nonvolatile memory devices.