Toxicity of quantum dots (QDs) has been a hot research concern in the past decade, and there is a lot of challenge in this field. The physicochemical characteristics of QDs can affect their toxicity, while little is known about the specific chemical form of QDs in living cells after incubation so far. In this work, speciation of four CdSe/ZnS QDs in HepG2 cells was carried out from the metallomics' point of view for the first time by using size exclusion chromatography (SEC) coupled with inductively coupled plasma-mass spectrometry (ICP-MS). On the basis of the signal of Cd, two kinds of chemical forms, named as QD-1 and QD-2, were observed in HepG2 cells incubated with CdSe/ZnS QDs. QD-1 was demonstrated to be a kind of QD-like nanoparticles, confirmed by chromatographic retention time, transmission electron microscopy (TEM) characterization, and fluorescence detection. QD-2 was demonstrated to be cadmium-metallothioneins complex (Cd-MTs) by reversed phase liquid chromatography (RPLC) synchronously coupled with ICP-MS and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF-MS) analysis. Meanwhile, speciation of QDs in HepG2 cells incubated with different conditions was analyzed. With the variation of QDs incubation concentration/time, and elimination time, the species of QD-1 and QD-2 were also observed without other obvious species, and both the amount of QD-1 and QD-2 increased with incubation concentration and time. The obtained results provide valuable information and a strategy for the study of existing chemical form of QDs, greatly benefiting the understanding of QDs toxicity in living cells.