Nanoreactors whose reactions are remotely controlled by magnetic fields are potentially valuable for bio-orthogonal chemistry for future use. Here develops a silicon-induced magnetotherm-induced nanoreactor (MAG-NER) by selectively increasing Pd nanocrystals on a pre-installed iron oxide core inside a hollow silicon nanocell. Growth is achieved by magnetic induction. The interfacial catalytic site is activated by stimulation of localized magnetotherm, while the nanopartmentalization is performed by means of selectively sized porous silicon. Therefore, MAG-NER can be comfortably used in complex biomedia and even its internal embodiment can be found in living cells. This work explains the design of advanced nanoreactors that complement and enhance existing bio-orthogonal chemical tools.