Quantum dots-induced cell growth inhibition effect and its photophysical mechanism were investigated in this report. Cell growth curve and atomic force microscopy show that QDs block cell division to inhibit the growth of bacterial cells. On the basis of combined biological and physical discoveries from cytochrome c reduction assay, hydrodynamic size, photoluminescence and UV-visible spectrometry, a photophysical mechanism involving a polypeptide or amino acid adsorption-mediated fluorescence and reactive oxygen species quenching process is proposed. The photophysical mechanism may not only provide physical insight of QDs-induced toxicity, but also render QDs potentials in antimicrobial and cancer photodynamic therapy applications.