We use molecular dynamics (MD) method to describe the atomic behavior of Graphene nanostructure for Oxygen molecules (O2) separation from Carbon dioxide (CO2) molecules. Technically, for the simulation of graphene-based membrane and O2-CO2 gas mixture, we used Tersoff and DREIDING force fields, respectively. The result of equilibrium process of these structures indicated the good stability of them. Physically, this behavior arises from the appropriate MD simulation settings. Furthermore, to describe the purification performance of graphene-based membrane, we report some physical parameters such as purification value, impurity rate, and permeability of membrane after atomic filtering process. Numerically, by defined membranes optimization, the purification value of them reach to 97.31%. Also, by using these atomic structures the CO2 impurity which passed from graphene-based membrane reach to zero value.