Monolayer functionalized ultra-small gold nanoparticles (AuNPs) provide a versatile platform for applications in cell research. Through rational design of surface ligands, the chemistry of AuNPs are precisely regulated at atomic level. In this dissertation, applications of AuNPs in cell modulation are discussed. The topics are split into two categories. In the first category, functionalized AuNPs are harnessed to generate a robust monolayer on cell culture surface for cell modulation. The proliferation and behavior of different types of cancer cells and normal cells are modulated by tuning the surface ligands of AuNPs. Fate decision of mesenchymal stem cells are also modulated using the same strategy. In the second category, AuNPs are assembled to nanoparticle stabilized capsules (NPSCs) for the delivery of a variety of proteins to cytosol of cells. Using this method, phenotype of cells are rapidly switched without genomic disturbance. In addition, subcellular localization of proteins are also controlled by the combination of subcellular localization signals and NPSC delivery platform. The first non-peptide synthetic nuclear localization signal based on boronate is discovered using NPSC delivery platform as well.