The size of real nanoparticles (NPs) is polydisperse which can influence the electrical property of polymer nanocomposites (PNCs). Here, we explored the percolated network of mixed NPs with different sizes (small NPs and big NPs) by adopting a molecular dynamics simulation. The simulated results reveal that the big NPs are adverse to building the percolated network compared to the small NPs. Thus, the percolation threshold becomes higher along with increasing the mixing ratio, which denotes the concentration ratio of big NPs to the total NPs. For a better understanding of it, the dispersion state and the number and the size of clusters are employed to analyze the percolated network, which can explain the percolation threshold well. Furthermore, by adopting the Sun’s theory (Macromolecules, 2009, 42, 459–463), small and big NPs exhibit a weak antagonistic effect in the simulation if their total concentration is fixed. On the one hand, the number of small NPs is larger than that of big NPs at the same concentration. In addition, one big NP can connect to more others than one small NP. These two contrast effects are responsible for it. Interestingly, the shear flow leads to more contact aggregation structure of NPs which is beneficial to build the new percolated networks. Especially, the big NPs play a more important role in forming the percolated network than small NPs. Consequently, the percolation threshold is reduced at a higher shear rate. In total, our research work provides a further understanding of how the mixed NPs with different sizes form the percolated network in polymer matrix.