Hollow mesoporous SiO(2) (mSiO(2)) nanostructures with movable nanoparticles (NPs) as cores, so-called yolk-shell nanocapsules (NCs), have attracted great research interest. However, a highly efficient, simple and general way to produce yolk-mSiO(2) shell NCs with tunable functional cores and shell compositions is still a great challenge. A facile, general and reproducible strategy has been developed for fabricating discrete, monodisperse and highly uniform yolk-shell NCs under mild conditions, composed of mSiO(2) shells and diverse functional NP cores with different compositions and shapes. These NPs can be Fe(3)O(4) NPs, gold nanorods (GNRs), and rare-earth upconversion NRs, endowing the yolk-mSiO(2) shell NCs with magnetic, plasmonic, and upconversion fluorescent properties. In addition, multifunctional yolk-shell NCs with tunable interior hollow spaces and mSiO(2) shell thickness can be precisely controlled. More importantly, fluorescent-magnetic-biotargeting multifunctional polyethyleneimine (PEI)-modified fluorescent Fe(3)O(4)@mSiO(2) yolk-shell nanobioprobes as an example for simultaneous targeted fluorescence imaging and magnetically guided drug delivery to liver cancer cells is also demonstrated. This synthetic approach can be easily extended to the fabrication of multifunctional yolk@mSiO(2) shell nanostructures that encapsulate various functional movable NP cores, which construct a potential platform for the simultaneous targeted delivery of drug/gene/DNA/siRNA and bio-imaging.