Recently, many studies of filler-filled rubbers using coarse-grained molecular dynamics simulation were reported, and many researchers are interested in these studies. We have contributed to the development of the OCTA system, which is the simulation system for high functional soft materials, and we have been applied OCTA to simulate the rubber materials. From our simulations of filler-filled rubbers, the physical properties of these materials are much affected by the dispersed structures. Therefore how to make the initial structure of the filler dispersed structures is one of the critical problems in our simulation studies. In this study, we developed the method to construct the initial structure for the coarse-grained molecular dynamics simulation for the filler-filled rubbers using the OCTA system. In our simulations, the different dispersed structures by the larger-scale-level simulations are used to construct the structures of coarse-grained molecular dynamics in which the fillers are dispersed. Using these structures, the physical properties are simulated by coarse-grained molecular dynamics method. These results will be explained in the session.