Filled vulcanizates exhibit the nonlinear Payne effect under dynamic deformations at high strain amplitudes, while the underlining mechanisms are still in dispute. Herein, polydimethylsiloxane (PDMS) networks are prepared via end-linking of alpha,omega-vinyl-terminated PDMS chains by the thiol-ene reaction, and the influences of silica on the dynamic rheological responses are investigated. The presence of silica tends to improve the crosslinking density alongside reinforcing the network, while silica itself does not contribute to the loss factor markedly. Furthermore, silica could promote the onset strain amplitude of the Payne effect and manifest the very weak overshoot of loss modulus near the onset amplitude. By creating master curves of the Payne effect of the filled vulcanizates referenced to the end-linking networks, it is evidenced that this effect and the accompanied weak overshoot are mainly rooted in the nonlinear Rouse dynamics of the network strands.