The quality and the efficacy of herbal medicine are of great concern especially with the increase in their global use. Medicinal plants of different species or collected from different geographical regions have shown variations in both their contents and pharmacological activities due to the differences in the environmental conditions of the collected sites. In this study, roots of Phytolacca acinosa found in different provinces in south China (Sichuan and Shandong) and a species of Phytolacca americana were investigated. To ensure a maximum yield of the major compounds, the extraction method and conditions were optimized. The preeminent method of extraction in this analysis was determined to be the ultrasound-assisted method with specific conditions as follows: ethanol-H2O (1:1, v/v), with a solvent: sample ratio of 1:8, and extraction was performed 3 times, each for 30 min. Under these conditions, samples from the different regions varied both in quantity and quality via the LC-MS analysis. A total of 60 triterpenoid saponins were detected within the three samples, among which 22 were identified as common in the three samples. The amounts of these common triterpenoid saponin identified varied across the samples. Moreover, the analysis led to the detection of some novel compounds that have not yet been reported in this family, while other compounds differ in their fragmentation pathways compared to previous literature. To further divulge the correlations between the bioactivities in these three samples and the quantity and quality of their bioactive components, a cytotoxic analysis was thus carried out with two cancer cell lines, and SGC-7901 and Hep G2, which evidently showed remarkable differences in their anti-proliferative activities with respect to the IC50 value. Samples of P. acinosa from Sichuan showed higher values in both cell lines (27.20 ± 1.60 and 25.59 ± 1.63 µg/mL) compared to those of Shandong and P. americana. For the first time, analysis and comparison of both interspecies and of different species in this family were carried out. This study will significantly contribute to the quality insurance of herbal medicine, especially in the Phytolaccaceae family.