Nanomaterials have been utilized in biomedical applications for many years because of their unique properties such as quantum confinement, surface plasmon resonance, and superparamagnetism. These applications are expected to advance diagnosis and therapeutics. Fluorescent nanomaterials, such as quantum dots (QDs), were exalted in biological imaging and tracking, and trended to replace protein-based probes. Our previous investigation indicated that cell-penetrating peptides (CPPs) are a promising delivery system that can translocate materials efficiently in a noncovalent manner. In this study, we demonstrate that arginine-rich CPPs can noncovalently complex with QDs and significantly raise efficiency of cellular entry. We further examined their mechanisms of cellular penetrations, subcellular localizations, and cytotoxicity. Importantly, CPP/QD complexes were not toxic at the level of efficient transduction. Collectively, our study provided an insight that CPPs can facilitate the delivery of nanomaterials into cells. Various compositions of CPPs are a major factor affecting uptake routes and efficiency for drug delivery applications.