Through coarse-grained molecular dynamics simulation, we aimed to uncover the rupture mechanism of the nanofiller filled polymer nanocomposites by characterizing the structural and dynamic changes during the tension process. We find that the strain at failure is corresponding to the coalescence of single void into larger voids, namely the change of the free volume. After the failure, the stress gradually decreases with the strain, accompanied by the contract of the highly orientated polymer bundles. The number of voids is quantified as a function of the strain, exhibiting a non-monotonic behavior because of the coalescence of small voids into larger ones at high strain. However, the number of voids is greatly reduced by a stronger interfacial interaction. Meanwhile, the new voids are formed where the chemical bonds are broken which again increases the number of voids at high cross-link density. At last, it decreases again because of the low rate of bond scission. In particular, with weak interfacial interaction, the nucleation of voids occurs in the interface, and in the polymer matrix in the strong case. With the interfacial interaction increasing, it induces the rupture transition from mode A (no bundles) to B (bundles). An optimal volume fraction of nanofillers exists for the stress-strain behavior, which can be rationalized by the formation of the strongest polymer-nanorod network. In addition, the rupture property first increases and then decreases with the increase of the grafting density, which can explained by the contribution of matrix chains, grafted chains, and nanofillers to the total stress. Last, we found that the chemical bonds are broken at the similar strain and the high broken percentage of bonds on the chain backbone happens for the uniform cross-link distribution which indicates the more homogenous stress distribution. In summary, this work could provide a clear understanding of the fracture mechanism of PNCs on the molecular level.