We present a new approach for the fabrication of thermoresponsive polymer microcapsules with mobile magnetic cores that undergo a volume phase-transition upon changing the temperature and are collected under an external magnetic field. We have prepared organic/inorganic composite microspheres with a well-defined core-shell structure that are composed of a crosslinked poly(N-isopropylacrylamide) (PNIPAM) shell and silica cores dotted centrally by magnetite nanoparticles. Since the infiltration of template-decomposed products is dependent on the permeability of PNIPAM shells triggered by changes of exterior temperature, the silica layer sandwiched between the magnetic core and the PNIPAM shell was quantitatively removed to generate PNIPAM microcapsules with mobile magnetic cores by treatment with aqueous NaOH solution. For development of the desired multifunctional microcapsules, modification of the unetched silica surface interiors can be realized by treatment with a silane coupling agent containing functional groups that can easily bind to catalysts, enzymes, or labeling molecules. Herein, fluorescein isothiocyanate (FITC), which is a common organic dye, is attached to the insides of the mobile magnetic cores to give PNIPAM microcapsules with FITC-labeled magnetic cores. In this system, it can be expected that an extension of the functionalization of the cavity properties of smart polymer microcapsules is to immobilize other target molecules onto the mobile cores in order to introduce other desired functions in the hollow cage.