Plants in the Genus Vernonia family (Asteraceae) contain physiologically active chemicals, making them ideal for discovering and developing anticancer medicines. Hepatocellular carcinoma (HCC), one of the most recognized cancers in the world, is on the rise, with a high mortality rate and a dismal prognosis. As a result, the treatment of HCC remains a splendid challenge. We aimed in this study to assess the cytotoxic activity of Vernonia leopoldii extracts in the HepG2 cell line. By extractions of V. leopoldii aerial parts from Yemen were collected, and the SRB assay was used to evaluate their cytotoxicity against liver cancer cell line (HepG2) and normal liver cell line (BNL), calculating the half-maximal growth inhibitory concentration. Metabolite profiling of the total methanolic extract of V. leopoldii was carried out for the first-time using LC-MS/MS in positive mode to investigate its chemical composition. Moreover, flow cytometry analysis was used to quantify the cell cycle arrest, apoptotic/necrotic, and autophagic cell death in the treated HepG2 cancer cells. A scratch assay was performed to examine the effect of the methanolic extract on HepG2 cell migration. We found MeOH extract was more cytotoxic against HepG2 cells (IC50= 9.2 ± 0.88 µg/mL) compared to methanol/water extract (IC50 > 100 µg/mL), with less cytotoxicity in BNL cells (IC50 = 85.9 ± 2.3 µg/mL). The LC-MS/MS analysis of MeOH extract tentatively identified thirty-five chemical compounds, including one anthocyanin glycoside, eight flavones, one flavanone, five flavonol glycosides, two furanocoumarins, four phenolic acids, one sesquiterpene ester, and thirteen sesquiterpene lactones. The MeOH extract induced G2/M cell cycle arrest along with apoptotic and autophagic cell death in HepG2 cells. Moreover, this extract inhibited HepG2 migration, as shown in the scratch healing assay. These findings provide interesting new information about how V. leopoldii induces apoptotic/autophagic, anti-migratory, and anti-proliferative cell death in HepG2 cells, which may be able to lessen the aggressiveness of HCC.