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 Hg3Se2Cl2. 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.