A computational study based on molecular dynamics simulation technique has been used to predict the mechanical and thermal behavior of carbon nanotube (CNT) reinforced natural rubber (NR) composites. A single-walled 5,5 armchair type CNT has been used for this purpose. In this study, a comparison has been made between pristine and functionalized CNTs. The functionalization groups used in this study were carboxylic (COOH), ester (COOCH3) and hydroxyl (OH). The studies show the improvement in elastic properties of developed composites in the presence of functionalization group. In addition, the effect of volume fraction and 1-25% addition of functionalization group has been studied. The obtained simulation results show the better load-transfer capacity in developed polymer system and improved elastic modulus. Thermal properties of developed composite systems were studied by non-equilibrium molecular dynamics method (NEMD). The addition of functionalized CNTs shows enhanced mechanical and thermal properties.