Ultra-fine Au nanoparticles (NPs) show great application potential in catalysis. Size-tunable Au NPs have been fabricated on MoS(2) covered with monolayer 3,4,5,10-perylene tetracarboxylic dianhydride (PTCDA), and the morphological evolution as a function of Au deposition amount was investigated using scanning tunneling microscopy (STM). The PTCDA molecules act as a surfactant to stabilize ultra-fine Au NPs. Molecular scale STM images show that on MoS(2) the Au NPs with PTCDA molecules on top can be formed with height and lateral size down to 1.3 nm and 3.5 nm, respectively. By controlling the deposition amount and annealing temperature, the size of Au NPs can be tuned. After annealing at 270 °C to remove PTCDA, Au NPs with a linear size ≤5 nm can be obtained on MoS(2)(0001), facilitating the characterization of their intrinsic physical and chemical properties using various analytical techniques. In addition, photoemission spectroscopy data reveal charge transfer from Au NPs to PTCDA, indicating that the NPs possess more reactive chemical properties than bulk Au.