Cadmium ion (Cd 2+ ) is a common environmental pollutant with high biotoxicity. Interestingly, the Cd 2+ biotoxicity can be alleviated by the coexisting selenite (SeO 3 2− ), which induces the formation of cadmium selenide-rich nanoparticles (CdSe NPs) under the function of thiol-capping peptides. However, the detailed biochemical mechanisms by which Cd and Se are synergistically transformed into CdSe NPs in living organisms remain unclear so far.Here, we shed light on the molecular basis of such biotransformation processes in Caenorhabditis elegans by focusing on the roles of several key thiol-capping peptides. By monitoring the compositional and structural changes of the Cd and Se species and the genetic-level responses of nematodes, we revealed the specific roles of glutathione (GSH) and phytochelatins (PCs) in mediating the CdSe NP formation. With the aid of in vitro bioassembly assay and density functional theory calculations, the detailed Cd−Se interaction pathways were further deciphered: the ingested Cd binds predominantly to GSH and PCs in sequence, then further interacts with selenocysteine to form tetrahedral-structured PC2−Cd 2 −Sec 2 complex, and ultimately grows into CdSe NPs. This work provides molecular-level insights into the Cd−Se interaction in C. elegans and lays a basis for controlling the ecological and health risks of heavy metals in polluted environment.