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 HgCl 2 -induced structural transformation of amorphous selenium nanoparticles (SeNPs) with the main composition of Se 8 . Owing to the high binding affinity with selenium and coulomb interactions, Hg 2 + ions can permeate into the interior of SeNPs, making the amorphous Se 8 turn to polycrystalline Hg 3 Se 2 Cl 2 . As a proof of concept, SeNPs then serve as a highly effective scavenger for selective removal of Hg 2 + 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.