The demand for truck–bus radial (TBR) tires with enhanced fuel efficiency has grown in recent years. Many studies have investigated silica-filled natural rubber (NR) compounds to address these needs. However, silica-filled compounds offer inferior abrasion resistance compared to carbon black-filled compounds. Further, the use of NR as a base rubber can hinder silanization and coupling reactions due to interference by proteins and lipids. Improved silica dispersion be achieved without the use of a silane coupling agent by introducing epoxide groups to NR, which serve as silica-affinitive functional groups. Furthermore, the coupling reaction can be promoted by facilitating chemical interaction between the hydroxyl group of silica and the added epoxide groups. Thus, this study evaluated the properties of commercialized NR, ENR-25, and ENR-50 compounds with or without an added silane coupling agent, and the filler–rubber interaction was quantitatively calculated using vulcanizate structure analysis. The increased epoxide content, when the silane coupling agent was not used, improved silica dispersion, abrasion resistance, fuel efficiency, and wet grip. Once a basic level of silica dispersion was secured by using the silane coupling agent, both the abrasion resistance and wet grip improved with increasing epoxide content. Furthermore, the silane coupling agent could be partially replaced by ENR due to the high filler–rubber interaction between the ENR and silica. Therefore, epoxidation shows potential for resolving the issues associated with poor coupling reactions and abrasion resistance in silica-filled NR compounds.