In this study, we suggest a unique approach with which it is possible to enhance the capacity and cycle performance of composite anode materials for lithium ion batteries. We introduced surface thiol groups onto mesocarbon microbeads (MCMB), and these functional groups efficiently obstructed the agglomeration between Sn nanoparticles in the composite formation. This resulted in the high dispersion of Sn nanoparticles with very small size. Half-cell tests showed that highly dispersed Sn nanoparticles enabled us to enhance the capacity by improvement of mechanical stress tolerance in the charge/discharge process.