Good dispersion of silica filler in the rubber matrix is a key factor for the high-performance properties of rubber/silica nanocomposites. This work aimed at using mild and green conditions for incorporating high silica content in natural rubber (NR) without using a silane coupling agent. The NR latex was modified into a low degree (5%) of epoxide-functionalized NR, symbolized as ENR5 by epoxidation reaction. The silica (40 phr) was pre-dispersed in water using ultrasonication to break down the silica particles, symbolized as USiP before mixing in the obtained ENR5 latex. After water evaporation, no silica flocculation at the bottom of the container was observed, meaning that silica was well infiltrated in the rubber matrix without coagulating agents. The interaction of hydroxyl groups of silica with epoxide groups of ENR5 could support the stable dispersion of the silica in the rubber matrix. Then, the dried ENR5-USiP was further mixed with curing agents in a two-roll mill. The cure characteristic, morphology and mechanical properties of ENR5-USiP were compared with silica-filled NR using a conventional mixing process (NR-SiC) and NR filled with silica treated by a silane coupling agent (NR-SSiC). As a result, ENR5-USiP exhibited higher mechanical properties than NR-SiC and NR-SSiC. The SEM micrograph revealed the good dispersion of nano-size silica in the rubber matrix of ENR5-USiP composites. It can be highlighted that the breakage of silica particles by ultrasonication is a facile method and mixing of the obtained silica in the ENR5 latex is a green condition. Furthermore, the possible interaction between the silanol groups of silica and epoxide functional groups of ENR5 could play an important role in improving the mechanical properties of the silica-filled rubber composites without requiring a silane coupling agent.