AbstractGold(I)‐thiolate complexes have served as primary building blocks for diverse Au nanostructure synthesis strategies. A delicate approach to characterize and control Au(I)‐thiolate motif formation and assembly on the surface is needed as it can potentially solve challenges associated with utilizing gold nanomaterials in many applications. Here, the controllable generation of flower‐shaped surface gold nanostructures (FSGNs) is demonstrated by manipulating the formation‐assembly process of Au(I)‐dodecanethiolate motifs within nanoscale surface droplets. The morphology and structure of the resulting Au nanostructures are governed by internal convection flows and interfacial energy, modulated by the nanodroplet composition and substrate wettability. The obtained FSGNs are proven to act as versatile scaffolds for the selective generation of Au spiky nanostars. These FSGNs can also be utilized to functionalize nanodroplet‐based reactors, boosting the fluorescent intensity of Nile red (NR) fluorophores and decomposing NR via catalytic reaction. Remarkably, with FSGN functionalized droplets smaller than a radius of 500 nm, the decomposition rate of NR can reach ≈0.01 s⁻¹. These results highlight a miniaturized, controllable, and automated method for the in situ production of 3D gold nanostructures on substrates, offering prospects for fast surface nanostructure fabrication and efficient environmental pollutant treatment.