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Modification of fillers and enhancement of the dispersion and compatibility of fillers in a rubber matrix is an effective way to improve the comprehensive performance of rubber. In this work, graphene oxide (GO) was modified with each of polyvinylpyrrolidone, 1‐allyl‐3‐methylimidazole hydrochloride and 1‐butyl‐3‐methylimidazole hexafluorophosphate. Then, modified GO/natural rubber (NR) composites were fabricated using a latex‐mixing method. By combining experiments and molecular simulation, we investigated the relationship between the microstructures and properties of the modified GO/NR composites. Results showed that the polyvinylpyrrolidone‐modified GO/NR composite had the smallest fractional free volume and mean square displacement, which led to excellent solvent resistance, and dynamic and physical mechanical properties. This study provides new insights into the design of high‐performance GO/NR composites at the molecular level. © 2022 Society of Industrial Chemistry. [ABSTRACT FROM AUTHOR]