Yolk/shell nanoparticles (NPs), which integrate functional cores (likes Fe₃O₄) and an inert SiO₂ shell, are very important for applications in fields such as biomedicine and catalysis. An acidic medium is an excellent etchant to achieve hollow SiO₂ but harmful to most functional cores. Reported here is a method for preparing sub-100 nm yolk/shell Fe₃O₄@SiO₂ NPs by a mild acidic etching strategy. Our results demonstrate that establishment of a dissolution–diffusion equilibrium of silica is essential for achieving yolk/shell Fe₃O₄@SiO₂ NPs. A uniform increase in the silica compactness from the inside to the outside and an appropriate pH value of the etchant are the main factors controlling the thickness and cavity of the SiO₂ shell. Under our "standard etching code", the acid-sensitive Fe₃O₄ core can be perfectly preserved and the SiO₂ shell can be selectively etched away. The mechanism of regulation of SiO₂ etching and acidic etching was investigated.