Nanosecond pulse micro-discharges at atmospheric pressure have garnered attention because of their unique physics and numerous applications. In this study, we employed a one-dimensional particle-in-cell/Monte Carlo collision model coupled with an external circuit, using an unequal weight algorithm to investigate the breakdown processes in micro-discharges driven by pulses with voltage ranging from 1 kV to 50 kV at atmospheric pressure. The results demonstrate that nanosecond pulse-driven microplasma discharges exhibit different breakdown modes under various pulse voltage amplitudes. We present the discharge characteristics of two modes: ‘no-breakdown’ when the breakdown does not occur, and ‘runaway breakdown mode’ and ‘normal breakdown mode’ when the breakdown does happen. In the runaway breakdown mode, the presence of runaway electrons leads to a phenomenon in which the electron density drops close to zero during the pulse application phase. Within this mode, three submodes are observed: local mode, transition mode, and gap mode, which arise from different secondary electron generation scenarios. As the pulse voltage amplitude increases, a normal breakdown mode emerges, characterized by the electron density not dropping close to zero during the pulse application phase. Similarly, three sub-modes akin to those in the runaway breakdown mode exist in this mode, also determined by secondary electrons. In these modes, we find that electron loss during the pulse application phase is dominated by boundary absorption, whereas during the afterglow phase, it is dominated by recombination. Ion losses are primarily governed by recombination. These findings contribute to a better understanding of the discharge mechanisms during the breakdown process.