The objective of this study is to find new selective allelochemicals for managing two problematic weeds redroot pigweed (Amaranthus retroflexus) and common lambsquarters (Chenopodium album) with minimal negative effects on wheat, thereby facilitating the development of eco-friendly botanical herbicide. Three new sesquiterpenoids, sonarvenolide A–C (1–3), and nine known sesquiterpenoids (4–12) were isolated from Sonchus arvensis. Compound 1was a rare peroxide-substituted eudesmane-type sesquiterpenoid, and compound 3was a rare iphionane-type sesquiterpenoid. Notably, compounds 1, 3, 4, 6–8, and 11showed selectivity phytotoxic activity. In particular, compounds 1, 3, and 4exhibited excellent germination inhibitory effect on A. retroflexus(IC50= 32.0–129.0 μM), higher than that of the positive control triasulfuron (IC50= 141.7 μM), and compound 4showed excellent inhibition on C. album(IC50= 82.0 μM), higher than that of triasulfuron (IC50= 100.9 μM). In addition, compounds 1, 3, and 4showed allelopathy to the growth of two weeds, which were more potent than or close to that of triasulfuron. Furthermore, these compounds were not toxic to wheat even at a high concentration (1000 μM). Structure–activity relationships (SARs) revealed that the presence of peroxides or the absence of hydroxyl at C-5 in the eudesmane-type sesquiterpenoids could strengthen the inhibitory activities. The discovery of selective allelochemicals provides not only a new choice to control two problematic weeds of wheat but also new natural lead compounds for herbicides.