In this study, a room temperature NH3 bubble templating technique is developed to prepare zinc hydroxystannate [ZnSn(OH)6] hollow core-shell microspheres. Then, via a hydrothermal recrystallizing process, ZnSn(OH)6 hollow core-shell microcrystals with polyhedral morphology can be successfully obtained. It was found that the concentration of NH4F plays a crucial role in the morphology of the product. The optimal condition for the formation of hollow core-shell ZnSn(OH)6 microcrystals is that the concentration of NH4F is at 0.25 mol L−1 while the concentration of NaOH is fixed at 0.25 mol L−1. Reaction time has also a great influence on the morphology of the product. With the reaction time prolonged, hollow core-shell ZnSn(OH)6 microspheres would gradually crystallize into hollow core-shell ZnSn(OH)6 polyhedral microcrystals. The samples have been characterized by means of X-ray power diffraction (XRD), field emission scanning electron microscopy (FESEM), X-ray photoelectron spectra (XPS), selected area electron diffraction (SAED) and transmission electron microscopy (TEM). The formation mechanism of the ZnSn(OH)6 hollow core-shell microcrystals with polyhedral morphology has been discussed based on the experimental results.