Enzyme-loaded magnetic polyelectrolyte multilayer nanotubes prepared by layer-by-layer assembly combined with the porous template could be used as biomimetic nanoreactors. It is demonstrated that calcium carbonate can be biomimetically synthesized inside the cavities of the polyelectrolyte nanotubes by the catalysis of urease, and the size of the calcium carbonate precipitates was controlled by the cavity dimensions. The metastable structure of the calcium carbonate precipitates inside the nanotubes was protected by the outer shell of the polyelectrolyte multilayers. These features may allow polyelectrolyte nanotubes to be applied in the fields of nanomaterials synthesis, controlled release, and drug delivery.