Objective: The quantum dots are the useful materials in microelectronics and biomedical research. However its toxicity has to be considered. We studied the effect of cell inhibition with ZnS core quantum dots and CdTe quantum dots modified with Thioglycolic acid or Cysteine functional group (TGA-CdTe, TGA-CdTe/ZnS, Cys-CdTe, Cys-CdTe/ZnS) on Caco-2 cell proliferation. Methods: We studied the effect of cell inhibition with ZnS core QDs and CdTe QDs modified with functional group on Caco-2 cell proliferation by MTT assay at 0, 12.5, 25, 50, 100 μg/ml and 6, 24, 48 h. Result: Our results showed that all QDs have inhibited cell proliferation and reached maximum 79.21%. The inhibition rate of Cys-modified QDs increased with the increase of concentration and reached maximum 66.72%. The inhibition rate of TGA-modified QDs increased with the increase of time. The ratios of Cys-modified to TGA-modified were less than 1 at all concentrations and three exposure times (P ≤ 0.01). The average ratios of Cys-CdTe/ZnS to Cys-CdTe reached 1.11 only for 48 h (P ≤ 0.05). The ratios of TGA-CdTe/ZnS to TGA-CdTe were closed to 1 at all concentrations and exposure times. Conclusion: The regularity of QDs modified with functional group is that inhibition of TGA-modified higher than Cys-modified. Inhibition exhibited dose-dependent for Cys-modified while exhibited time-dependent for TGA-modified. The regularity of CdTe-QDs with ZnS or not is that the inhibition of Cys-CdTe/ZnS was higher than Cys-CdTe while TGA-CdTe/ZnS and TGA-CdTe were consistent.