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The Mongolian rhubarb—<i>Rheum undulatum</i> L. <i>(RU)</i>—and <i>Rumex crispus</i> L. <i>(RC)</i>—a Taiwanese local rhubarb belonging to the family of <i>Polygonaceae</i>—are principal therapeutic materials in integrative medicine due to their rich quantities of bioactive compounds; however, their phytochemical and antioxidant properties, and anti-cancer activity is poorly investigated. Furthermore, the phytochemical characteristics of both species may be affected by their different geographical distribution and climatic variance. The current study aimed to compare <i>RU</i> with <i>RC</i> extracts in different polarity solvents (n-hexane, ethyl acetate, acetone, ethanol, and water) for their phytochemical contents including the total phenolic content (TPC), total anthraquinone content (TAC), total flavonoid content (TFC), antioxidant and free radical scavenging capacities, and anticancer ability on the HepG2 cell. Except for the n-hexane extract, all of the <i>RU</i> extracts had considerably higher TPCs than <i>RC</i> extracts, ranging from 8.39 to 11.16 mg gallic acid equivalent (GAE) per gram of dry weight, and the TPCs of each extract were also significantly correlated with their antioxidant capacities by ABTS, DPPH, and FRAP assays (<i>p</i> < 0.05). Moreover, there was no remarkable association between the antioxidant capacities and either TACs or TFCs in both the <i>RU</i> and <i>RC</i> extracts. Besides, high-performance liquid chromatography (HPLC) analysis revealed that both the <i>RU</i> and <i>RC</i> extracts contained chrysophanol, emodin, and physcion, and those bioactive compounds were relatively higher in the n-hexane solvent extracts. Additionally, we observed different levels of dose-dependent cytotoxic effects in all the extracts by cell viability assay. Notably, the ethanol extract of <i>RU</i> had a compelling cytotoxic effect with the lowest half-maximum inhibition concentration (IC50-171.94 ± 6.56 µg/mL at 48 h) among the <i>RU</i> extracts than the ethanol extract of <i>RC</i>. Interestingly, the ethanol extract of <i>RU</i> but not <i>RC</i> significantly induced apoptosis in the human liver cancer cell line, HepG2, with a distinct pattern in caspase-3 activation, resulting in increased PARP cleavage and DNA damage. In summary, Mongolian Rhubarb, <i>RU</i>, showed more phytochemical contents, as well as a higher antioxidant capacity and apoptotic effect to HepG2 than RC; thus, it can be exploited for the proper source of natural antioxidants and liver cancer treatment in further investigation.