In this study, coarse-grained molecular dynamics (CGMD) simulations of polymer network gels filled with spherical nanoparticles (NPs) were performed, and two-dimensional (2D) small-angle scattering patterns of the NPs during uniaxial elongation were examined. To create filled polymer network gels, mixtures of polymer chains, four-arm star chains, and NPs, and pseudo-reaction processes were considered. Active sites of the polymer chains, four-arm star chains, and surface particles of the NPs were reacted to create bonds. After this pseudo-reaction process, it was evaluated whether the obtained polymer network was a sol or gel. The gel polymer network obtained in this study was not percolated as a graph but was able to transmit force through catenane-like linkages. This paper named this gel as "topological-percolation". Further, 2D scattering patterns (2DSPs) were calculated using three-dimensional fast Fourier transformation for efficient computing on a large-scale system. The obtained 2DSPs were quite different for the sol and gel, and depended on the properties of the crosslinked polymer networks. It is confirmed that changes in 2DSPs can be predicted by CGMD simulations because different patterns can be observed with different pre-polymer distributions, different chain lengths, and different chain densities.