In this work we perform molecular-dynamics simulations, both on the coarse-grained and the chemistry-specific levels, to study the influence of morphology on the mechanical properties of polymer nanocomposites (PNCs) filled with uniform spherical nanoparticles (which means without chemical modification) and patchy spherical nanoparticles (with discrete, attractive interaction sites at prescribed locations on the particle surface). Through the coarse-grained model, the nonlinear decrease of the elastic modulus (G′) and the maximum of the viscous modulus (G″) around the shear strain of 10% is clearly reproduced. By turning to the polybutadiene model, we examine the effect of the shear amplitude and the interaction strength among uniform NPs on the aggregation kinetics. Interestingly, the change of the G′ as a function of the aggregation time exhibited a maximum value at intermediate time attributed to the formation of a polymer-bridged filler network in the case of strong interaction between NPs. By imposing a dynamic periodic shear, we probe the change of the G′ as a function of the strain amplitude while varying the interaction strength between uniform NPs and its weight fraction. A continuous filler network is developed at a moderate shear amplitude, which is critically related to the interaction strength between NPs and the weight fraction of the fillers. In addition, we study the self-assembly of the patchy NPs, which form the typical chain-like and sheet-like structures. For the first time, the effect of these self-assembled structures on the viscoelastic and stress–strain behavior of PNCs is compared. In general, in the coarse-grained model we focus on the size effect of the rough NPs on the Payne effect, while some other parameters such as the dynamic shear flow, the interaction strength between NPs, the weight fraction, and the chemically heterogeneous surface of the NPs are explored for the chemistry-specific model.