This work investigates the compatibility of ten commercially available accelerators and ten antioxidants with three types of rubber by using molecular dynamics simulation. By constructing fully atomistic models of rubber and small molecules, firstly, the length and number of polymer chains, as well as the number of small molecules are optimized by calculating the solubility parameter. All simulated systems are guaranteed to reach equilibrium by checking the change of the density and energy. Then this work shows that the simulated results match well with each other, which are obtained from the value and the difference of the binding energy of the rubber systems, fractional free volume of the rubber systems, and self-diffusion coefficient of small molecules calculated from the mean square displacement-time curve. And some small molecules which are more compatible with rubbers are found. More importantly, this study can further determine their compatibility preference by calculating the partition coefficients of small molecules in the rubber blends. Meanwhile, the temperature effect on the change of the compatibility is as well examined. In general, this work provides some guidance for determining the compatibility between rubber and small-molecule additives, enabling the design of high-performance rubber materials.