This study aimed to investigate the inhibitory effect of the isothiocyanate derivatives from Moringa oleifera seeds (MITC-21) on the growth and migration of colon cancer HCT-116 cells. Changes in cell proliferation, apoptosis, migration and protein expression levels of HCT-116 cells treated with different concentrations of MITC-21 were determined by the MTT assay, colony formation assay, flow cytometry, wound-healing assay and western blotting. The results showed that MITC-21 treatment decreased significantly the viability of HCT-116 cells in a dose- and time-dependent manner, with the IC50 values for MITC-21 against HCT-116 cells for 24, 48 and 72 h being 6.79 µmol/L, 3.71 µmol/L, and 1.13 µmol/L, respectively. The results of the colony formation assay indicated that MITC-21 (0, 2 and 4 µmol/L) significantly decreased the colony-forming ability of HCT-116 cells and after a 48 h treatment, the colony formation rate decreased from 100% to 68.36% (p<0.05) and 49.51% (p<0.01). When MITC-21 was at 4 µmol/L, the cell morphology of HCT-116 cells changed significantly. Flow cytometry analysis showed that the apoptosis rate of HCT-116 cells increased with an increase of the dose and time of MITC-21 treatment. After a 48 h treatment, compared with that of the control cells (14.97%), the apoptosis rate of MITC-21-treated groups increased to 21.60% (p<0.001) and 22.78% (p<0.001), respectively. The wound-healing assay revealed that MITC-21 significantly inhibited the migration of HCT-116 cells, with the cell migration rate decreasing from 61.53% to 32.89% (p<0.01) and 24.30% (p<0.001), respectively. MITC-21 at 4 µmol/L significantly increased the Bax/Bcl-2 ratio and decreased the expression levels of the cell migration-related proteins MMP2. Thus, MITC-21 can inhibit the proliferation, induce apoptosis and suppress migration of HCT-116 cells.