In this work, by employing a coarse-grained molecular dynamics simulation, we have investigated the effect of the nanorod (NR) stiffness on the relationship between the NR microstructure and the conductive probability of NR filled polymer nanocomposites (PNCs) under the quiescent state and under the shear field. The conductive probability of PNCs is gradually enhanced with the increase of NR stiffness in the quiescent state; however, it first increases and then decreases under the shear field. As a result, the largest conductive probability appears at moderate NR stiffness, which results from the competition between the improved effective aspect ratio of the NR and the breakage of the conductive network.Meanwhile, compared with in the quiescent state, under the shear field the decrease or the increase of the conductive probability depends on the NR stiffness. At low NR stiffness, the increase of the effective aspect ratio of NR enhances the conductive probability, while at high NR stiffness, the breakage of the conductive network reduces the conductive probability. For flexible NRs, the conductive probability first increases and then decreases with increasing the shear rate. The maximum effective aspect ratio of NRs appears at the moderate shear rate, which is consistent with the conductive probability. In summary, this work presents some further understanding about how NR stiffness affects the electric conductive properties of PNCs under the shear field.