We demonstrate that binary mixtures of small and large gold nanoparticles (GNPs) (5/15, 5/30, 10/30, and 15/30 nm in diameter) in the presence of a glucose-terminated fluorinated oligo(ethylene glycol) ligand can spontaneously form size-segregated assemblies. The outermost layer of the assembly is composed of a single layer of small-sized GNPs, while the larger-sized GNPs are located in the interior, forming what is referred to as a yolk/shell assembly. Time course study reveals that small and large GNPs aggregate together, and these kinetically trapped aggregations were transformed into a size-segregated structure by repeating fusions. A yolk/shell structure was directly visualized in solution by X-ray laser diffraction imaging, indicating that the structure was truly formed in solution, but not through a drying process.