A simple method is proposed for the synthesis of noble metal M@YSiO2 (M = Au, Pd, Ag) yolk-shell nanoparticles. The effects of synthesis conditions on the preparation of yolk-shell nanoparticles were discussed in detail. According to the different corrosion resistances between inorganic silica and organosilicone in a selective etching solution, yolk-shell nanoparticles with large cavity and thin shell were prepared using the same aqueous medium in a step-by-step synthesis process. Different from traditional methods, this method is facile and efficient because the main synthesis process is carried out in an aqueous phase. This extended method may benefit the synthesis and application of other nanomaterials with a similar yolk-shell structure.