There is substantial progress along with giant debate in reinforcement mechanisms in relation to structured filler network and heterogeneously retarded polymer dynamics, while the dissipation behaviors have never been clarified for nanoparticle filled polymers. Herein dynamic rheological behaviors of silica filled natural rubber were investigated. Master curves of linear rheology in the hydrodynamic regime and those of the nonlinear Payne effect at a predetermined frequency were created, disclosing a leading role of dynamically retarded bulk rubbery phase to the hydrodynamic regime and a leading role of molecular disentanglement in the bulk phase to the Payne effect. The methodology is able to, account for both reinforcement and dissipation of the compounds as a function of filler content. Furthermore, a frequency-dependent hydrodynamic to non-hydrodynamic transition is revealed, revealing the importance of the relaxation of chains in the bulk phase to both reinforcement and dissipation of the compounds. It is suggested that the,dynamics of the bulk phase play a critical role for the rheology in the hydrodynamic regime while the fractal filler aggregates become dominative only in the terminal non-hydrodynamic regime where the bulk phase relaxes sufficiently.