Nanoparticles are known to self-assemble into large aggregates through interparticle and external forces. Understanding how interparticle interaction forces affect the construction and organization of nanomaterials is of growing importance to the development of the self-assembly technique. Current studies tend to focus on the individual factors and lack the collective effects from multiple forces as virus, lipid, or peptide does. The dual control on the self-assembly process of citrate-capped Au nanoparticles (AuNPs) mediated by the interparticle forces is reported. This self-assembly process is governed by the collective effects of both thiol-containing biomolecules and the ionic strength of dielectric medium. Thiol-containing biomolecules can effectively replace surface citrate molecules on AuNPs forming stable AuS bonds, leading to the lowering of surface potential or charge. Ionic strength of the solution can decrease the ion binding and the screening length of the double-layer repulsion. When these two factors are in play simultaneously, they collectively affect the AuNPs self-assembly process through the interparticle interactions by contributions from both factors, which have been interrogated based on the classical Derjaguin–Landau–Verwey–Overbeek theory. It is interesting to observe the existence of a quasi-stable state existed between two aggregated states, where two factors cancel each other and the AuNPs remain well dispersed, indicating that their concurrent effects are not simply additive. The results provide new insight to the assembly process of metal nanoparticles, and may open up new avenues to manipulate process.