The size of gold nanoparticle aggregates was controlled by manipulating the interparticle interaction. To manipulate the interparticle interaction of gold nanoparticles prepared by citrate reduction, we applied the substitutive adsorption of benzyl mercaptan on the particle surface in the absence of the cross-linking effect. Various experimental techniques such as UV-vis absorption spectroscopy, surface-enhanced Raman scattering, quasi-elastic light scattering, and zeta-potential measurement were used to characterize the nanoparticle aggregates. Our results suggest that the replacement of the trivalent citrate ions adsorbed on the nanoparticle surface with monovalent benzyl mercaptan ions should destabilize the particles, causing aggregation and hence the increase in the size of nanoparticle aggregates. These experimental results were successfully rationalized by the classical DLVO (Derjaguin-Landau-Vervey-Overbeek) theory that describes the interparticle interaction and colloidal stability in solution. Our findings suggest that the control of surface potential is crucial in the design of stable gold nanoparticle aggregates.