Quantum dots (QDs), including CdSe/ZnS, are nanoparticles emitting various wavelengths of fluorescent light depending on their size. Fluorescence allows them to be exploited for in vivo sensing/imaging of cancer cells. Nevertheless, thorough assessments of the effects of these commonly used QDs on cell stability are essentially required prior to their full applications. To investigate the effects of Cd QDs on the growth of human cervical cancer cells (HeLa), we utilized a growth assay, a reactive oxygen species (ROS) assay, an apoptosis assay, and RNA-seq. The growth assay results showed significant proliferation inhibition of HeLa cells by CdSe/ZnS. We revealed that smaller green CdSe/ZnS exerts more toxic effects than slightly larger yellow CdSe/ZnS. There were no significant increases of ROSs under the treatment of Cd QDs, which is consistent with the notion that low concentration of Cd QDs does not cause significant production of ROSs. In addition, we found that Cd QDs induced late apoptosis. RNA-Seq-based transcriptome analysis revealed that the exposure to green Cd QDs significantly upregulated antiapoptotic, antiproliferative, and antitumorigenic functions. The transcriptome profile also noted the downregulation of pro-proliferation, mitochondrial respiratory chain, detoxification, and receptor-mediated endocytosis. Taken together, our findings provide evidence that green CdSe/ZnS can be an alternative anticancer drug. In addition, our transcriptome analysis provides new insights into alteration of physiological state induced by CdSe/ZnS QDs in HeLa cancer cells.