It is very urgent to understand the rheological behavior of polymer nanocomposites (PNCs) on the molecular level, which is very important for their processing and application. Thus, here the reverse nonequilibrium molecular dynamics simulation isemployed to explore it by tuning the nanoparticle (NP) concentration, the polymer-NPinteraction and the NP size. The shear viscosity (η~-m) exhibits a power law with theshear rate where m varies from 0.42 to 0.53 at high shear rates. By adopting the Carreau-Yasuda model, the obtained zero-shear viscosity gradually rises with increasing the NPconcentration, polymer-NP interaction or reducing the NP size. This is attributed to thestrong adsorption of chains by NPs and the formed network, which leads to the retarded dynamics. In addition, both the first and second normal stress differences also show power laws on the shear rates. The chains are gradually extended as the increase of shear rates, which is characterized by the mean-square end-to-end distance and the mean square radius of gyration. Especially, the evolution process of the NP network and the polymer- NP network is analyzed to deeply understand the shear thinning behavior. The number ofthe direct contact structure of NPs increases while the number of polymer-NP bridgedstructure is reduced. This is further proved by the increase of the formation probability of the NP network and the decrease of the polymer-NP interaction energy. Finally, the chain dynamics is found to be enhanced due to the shear flow. In summary, this work provides a further understanding on the mechanism of the shear thinning of PNCs on the molecular level.