In this paper, we present a new method of fabricating metal nanoparticles on carbon substrates through molecular design. Scanning tunneling microscopy measurements show that the electrochemically synthesized Ag nanoparticles are homogeneously dispersed on the modified highly oriented pyrolytic graphite (HOPG) surface with a narrow particle size distribution. Moreover, the size and number density of Ag nanoparticles on the grafted HOPG surface can be easily changed through control of the experimental conditions.