Marine organisms contain several secondary metabolites with potent biological and pharmacological activities. This research aimed to study the cytotoxicity and mechanism of action of methanol (MeOH) extract from the exoskeleton (shell and spines) of the sea urchin Echinometra Mathaei on human liver cancer cell line (HepG2). E. mathaei was collected from the intertidal zone of the Red Sea, Al-Ain Al-Sokhna, Egypt. HepG2 cells were treated with the MeOH extract for 24 and 48 hours to assess the cytotoxic activity and the potential molecular mechanisms. The expression levels of apoptosis-, autophagy-, and cell proliferation-related genes and/or proteins were measured. In addition, metabolomic profiling of the extract was performed by gas chromatography-mass spectrometry (GC-MS) analysis. The extract displayed cytotoxic activity on the liver cancer cells (IC50 29.47 and 14.97 µg/ml at 24 and 48 hours, respectively). It induced apoptosis, autophagy and inhibited cell proliferation of HepG2 cells. The metabolomic profiling showed that the extract is rich in fatty acids. These results demonstrated that the exoskeleton MeOH extract of E. mathaei induced apoptosis in HepG2 cells, confirming its cytotoxic effect. Therefore, a thorough investigation of its molecular target and structure is necessary to develop novel anticancer therapeutics from marine Sea urchins.