Liver cancer is one of the leading causes of cancer-related deaths in the world. Bitter melon seed (BMS) is well known for anti-inflammatory and anticancer properties. MicroRNA-421 (miR-421) is considered as a regulator of cancer initiation, tumor metastasis, and progression, interfering with transcription of the mRNAs responsible for the cancer pathogenesis. HepG2 cells were treated with BMS water extract (BMSW) for 24 hr, and the IC50 was 586.27 ± 0.07 µg/ml. The ROS, mitochondrial membrane potential, the protein expression, and the nuclear fragmentation after the treatment of BMSW were respectively detected. The increase of ROS resulted in the decrease of mitochondrial membrane potential, which induced the apoptosis of cells subsequently. BMSW inhibited the proliferation of HepG2 cells by blocking cell cycle in the S phase and influenced the nuclei and the expression of protein, leading to cellular laxity and apoptosis. The expression level of miR-421 in HepG2 was distinctly down-regulated by 13.74 fold with 600 µg/ml of BMSW. Comprehensive microarray and RT-PCR analysis identified six putative target genes of miR-421 (GADD45B, DUSP6, DUSP3, DUSP10, CASP3, and CAPN2). The relationships of DUSP6, CASP3, and miR-421 were further confirmed by miR-421 mimics/inhibitor transfection by RT-PCR and western blot. The CASP3 was identified as target gene of miR-421. BMSW induced the apoptosis of HepG2 cell by regulating miR-421 and CASP3. PRACTICAL APPLICATIONS: Hepatocellular carcinoma (HCC) is a malignant tumour with the fourth highest mortality rate in the world. Bitter melon seed (BMS) as edible and medical food has significant anticancer activity. Our study indicated the anticancer mechanisms of BMS and provided the scientific basis for the application of BMS in healthy or novel functional foods. BMS can be used as dietary supplements or nutritional fortifiers to improve the survival status of patients with liver cancer due to safety and effectiveness.