The oil-paper insulation system will be affected by the synergistic effects of moisture and acids during long-term stable operation of the transformer. The moisture in the oil can be combined with the H+ionized from the acid molecules in the form of H3O+ by coordination, thus changing the proportion of acid distribution in the insulating oil and paper cellulose. Natural ester insulating oil, as a new development trend to replace mineral oil, can be significantly improved by adding nanoparticles to them. The diffusion behavior of H3O+ in paper cellulose and nano-SiO2-modified soybean oil-based natural ester insulating oil insulating system has been investigated using molecular dynamics in this article. The results indicate that the incorporation with nanoparticles is effective in mitigating the impact of temperature on the diffusion behavior of H3O+ in oil-paper insulation. Compared with the unmodified model, the nano-modified model results in a significant reduction in the concentration distribution of H3O+ in paper cellulose. The hydroxyl and ether bonds in paper cellulose will interact with H3O+ to generate hydrogen bonds and destroy its original hydrogen bonding network, while nanoparticles can inhibit diffusion by adsorbing H3O+ through hydroxyl oxygen atoms.