Elucidating the fouling phenomena of polymer surfaces will facilitate the molecular design of high-performance biomedical devices. Here, we investigated the remarkable antifouling properties of two acrylate materials, poly(2-methoxyethyl acrylate) (PMEA) and poly(3-methoxypropionic acid vinyl ester) (PMePVE), which have a terminal methoxy group on the side chain, via molecular dynamics simulations of binary mixtures of acrylate/methacrylate trimers with n-pentane or 2,2-dimethylpropane (neopentane), that serve as the nonpolar organic probe (organic foulants). The second virial coefficient (B2) was determined to assess the aggregation/dispersion properties in the binary mixtures. The order of the B2 values for the trimer/pentane mixtures indicated that the terminal methoxy group of the side chain plays an important role in enhancing the fouling resistance to nonpolar organic foulants. Here, we hypothesized that the antifouling properties of PMEA/PMePVE surfaces originate from the resistance. To evaluate the molecular-level accessibility of organic foulants to acrylate/methacrylate materials, we examined the radial distribution functions (RDFs) of the terminal methyl groups of neopentane around the main chains of the acrylate/methacrylate trimers. As a result, the third distinct RDF peaks are observed only for the methacrylate trimers. The peaks are attributed to the hydrophobic interactions between the methyl group of neopentane and that of the main chain of the trimer. Accordingly, the methyl group of the main chain of methacrylate materials, such as poly(2-hydroxyethyl methacrylate) and poly(2-methoxyethyl methacrylate), unfavorably induces fouling with organic foulants. In this study, we clarify that preventing hydrophobic interactions between an organic foulant and polymeric material is essential for enhancing the antifouling property. Our approach has great potential for evaluating the molecular-level affinities of organic foulant with polymer surfaces for the molecular design of excellent antifouling polymeric materials.