Intraparticle ion motions are critical to the structure and properties of nanomaterials, but rarely disclosed. Herein, in situ visualization of ion motions in a single nanoparticle is presented by dark-field microscopy imaging, which shows HgCl2 -induced structural transformation of amorphous selenium nanoparticles (SeNPs) with the main composition of Se8 . Owing to the high binding affinity with selenium and coulomb interactions, Hg2+ ions can permeate into the interior of SeNPs, making the amorphous Se8 turn to polycrystalline Hg3 Se2 Cl2 . As a proof of concept, SeNPs then serve as a highly effective scavenger for selective removal of Hg2+ ions from solution. This new finding offers visual proof for the photophysical process involving intraparticle ion motion, demonstrating that tracking the ion motions is a novel strategy to comprehend the formation mechanism with the purpose of developing new nanostructures like nanoalloys and nano metal compounds.