Rheological properties of three different nanocomposites, consisting of graphene oxide (GO), reduced graphene oxide (rGO), and polyhedral oligomeric silsesquioxane grafted reduced graphene oxide (rGO-POSS) as nanofillers and polydimethylsiloxane (PDMS), were investigated by large amplitude oscillatory shear (LAOS). The viscoelastic nonlinearity of the three nanofluids groups was studied by Lissajous curves, local nonlinear viscoelastic moduli of an oscillatory shear cycle, and Fourier transform rheology as a function of filler concentration and increasing and decreasing strain magnitude. The nonlinear behavior of the nanofluids was compared to understand the variation of internal microstructures. Firstly, GO/PDMS composites behave with higher moduli and smaller linear viscoelastic range comparing to that of other two composites. Secondly, the elastic stress Lissajous curves of these composites changed from elliptic to rectangular with round the corner with increasing the filler level and strain amplitude. Thirdly, all these three nanofluids exhibited intra-cycle strain stiffening with increasing strains and shear thickening at intermediate strain and then shearing thinning with increasing strain further. Fourthly, higher harmonic intensity of rGO/PDMS increased with increasing strain and came to a plateau, while that of other two nanofluids reached a maximum and then decreased. It suggested that different surface functionalization of nanoparticles will present different rheological behavior due to formed different network and LAOS could be used as a potential helpful method to characterize rheological properties of nanocomposites, especially at higher shear strain.