The aim of this study was to determine the content of triterpenoids and polyphenols, and antioxidative activity in leaves, stalks, and roots of plants from the species Fallopia as well as to present the main relationship between them. Polyphenolic compounds and triterpenoids were identified with liquid chromatography-photodiode detector-mass spectrometry/quadrupole time of flight (LC-MS-Q/TOF; qualitatively) and quantified with an ultra-performance liquid chromatography-photodiode detector (UPLC-PDA (quantitatively), and their antioxidative activity was determined with radical scavenging capacity (ABTS) and oxygen radical absorbance capacity (ORAC) assays. Generally, the wild Fallopia japonica Houtt. species had 1.2 times higher content of bioactive compounds and antioxidative activity than Fallopia sachalinensis. Contents of polyphenolic compounds determined in leaves, stalks, and roots were on average 17.81, 10.60, and 9.02 g/100 g of dry weight (DW), whereas the average contents of triterpenoids reached 0.78, 0.70, and 0.50 g/100 g DW, respectively. The leaves were a better source of polymeric procyanidins, phenolic acids, flavones, and flavonols, as well as oleanolic and ursolic acids than the other morphological parts of the tested plants. However, the roots were an excellent source of flavan-3-ols (monomeric and oligomer) and stilbenes, such as resveratrol, and their derivatives. The results obtained showed significant differences between plants of the wild Fallopia species and their morphological parts, and enabled selecting the most valuable morphological part of the tested plants to be used for food enrichment and nutraceuticals production. Therefore, the leaves seem to be the best as potential food additives for health, due to the above-average content of polyphenolic compounds and triterpenoids. In turn, roots, with their high contents of stilbenes and polyphenolic compounds, represent a good material for the medical, pharmaceutical, and cosmetic industries. The principal component analysis of the plants of wild Fallopia species and their morphological parts confirmed significant differences in their chemical composition.