This study is the first report on the preparation of mesoporous carbon/silica (MCS) nanocomposites with tunable mesoporosity and hydrophobicity using natural rubber (NR) as a renewable and cheap carbon source. A series of mesoporous nanocomposites based on NR and hexagonal mesoporous silica (HMS) were prepared via an in situ sol-gel process and used as precursors; then, they were converted into MCS materials by controlled carbonization. The NR/HMS precursors exhibited a high dispersion of rubber phase incorporated into the mesostructured silica framework as confirmed by small-angle X-ray scattering and high-resolution transmission electron microscopy. An increase in the carbonization temperature up to 700 °C resulted in MCS nanocomposites with a well-ordered mesostructure and uniform framework-confined wormhole-like channels. The NR/HMS nanocomposites possessed high specific surface area (500-675 m2 g-1) and large pore volume (1.14-1.44 cm3 g-1). The carbon content of MCS (3.0-16.1 wt%) was increased with an increase in the H2SO4 concentration. Raman spectroscopy and X-ray photoelectron spectroscopy revealed the high dispersion of graphene oxide-like carbonaceous moieties in MCS materials; the type and amount of oxygen-containing groups in obtained MCS materials were determined by H2SO4 concentration. The enhanced hydrophobicity of MCS nanocomposites was related to the carbon content and the depletion of surface silanol groups, as confirmed by the water sorption measurement. The study on the controlled release of diclofenac in simulated gastrointestinal environment suggests a potential application of MCS materials as drug carriers.