A universal method is reported for the synthesis of ligand free noble metal M@SiO (M = Ag, Au, Pd, Pt) yolk-shell nanoparticles (YSNs). Mesoporous hollow silica shells (mHSS) are used as smart nanoreactors for the synthesis of noble metal yolk-shell nanoparticles. The nanocavity of a mHSS and anionic metal ions play a critical role in the formation of yolk-shell nanoparticles. The synthesis mechanism can be tuned by simply varying the pH of the noble metal precursor aqueous solution. A critical pH ≥ 4 is required for the formation of YSNs. The anionic metal ions can pass freely through the mesopores of mHSS and eventually lead to the formation of YSNs, whereas the cationic metal ions can show strong interaction with the surface of mHSS which hinders the formation of YSNs. The syntheses of YSNs are achieved without using any external capping ligands and reducing agents in the reaction.