We review our recent studies of rubber system using coarse-grained molecular dynamics (CGMD) simulation. The CGMD simulation is one of the powerful tools to clarify the molecular chain dynamics of the rubber material in the deformation process. In this review, we show two topics listed below; the stretching of the rubber material in which the cross-linker is included, and the chain dynamics near the filler. In the first topics, we observe the chain conformation in the stretching. In this process, we can obtain the one or two strong force line of bonds. This nature indicates that the deformation of the rubber takes place in non-affine process in the nano-scale. In the second topics, we study the molecular motion near the filler, so called in the bound rubber layer. We construct the two models; the grafting chain model and the adsorbed chain model. We observe the local mean square displacement and the local glass transition temperature. We can observe that the chain moves slowly near the filler due to the restriction of the grafting or due to the attractive interaction between filler and polymer.