A novel natural rubber/silica (NR/SiO2) nanocomposite is developed by combining self-assembly and latex-compounding techniques. The results show that the SiO2 nanoparticles are homogenously distributed throughout NR matrix as nano-clusters with an average size ranged from 60 to 150 nm when the SiO2 loading is less than 6.5 wt%. At low SiO2 contents (⩽4.0 wt%), the NR latex (NRL) and SiO2 particles are assembled as a core-shell structure by employing poly (diallyldimethylammonium chloride) (PDDA) as an inter-medium, and only primary aggregations of SiO2 are observed. When more SiO2 is loaded, secondary aggregations of SiO2 nanoparticles are gradually generated, and the size of SiO2 cluster dramatically increases. The thermal/thermooxidative resistance and mechanical properties of NR/SiO2 nanocomposites are compared to the NR host. The nanocomposites, particularly when the SiO2 nanoparticles are uniformly dispersed, possess significantly enhanced thermal resistance and mechanical properties, which are strongly depended on the morphology of nanocomposites. The NR/SiO2 has great potential to manufacture medical protective products with high performances.