Protective waxes are typically mixtures of paraffin and microcrystalline waxes that retard the aging of unsaturated rubbers and are widely used in rubber products. The wax solubility of rubber products is important for understanding the migration behavior and film formation of waxes and determining the appropriate wax content in rubber compounds. In this article, protective waxes were applied to natural rubber (NR)/polybutadiene rubber (BR) based sidewall rubber and the compatibility between NR and BR and the protective wax dissolution in these rubbers were investigated with a focus on the former investigation through Materials Studio simulations. It was found that the simulation results are strongly correlated with the wax migration test results on compounded and cured rubber at different NR/BR mass ratios. Blends and mesoscopic dynamics simulations yielded good compatibility between NR and BR and favorable blend morphology. By analyzing the solubility parameter, R value, mean square displacement and diffusion coefficient of wax chains with different lengths in the NR/BR matrix, the mechanism and reasons for the wax precipitation variation of protective waxes at varying NR/BR mass ratios were analyzed from a microstructural point of view, which provides strong theoretical support for the design of the molecular structure of protective waxes.