A bioassay-directed phytochemical study was conducted to investigate potential allelochemicals in the roots of the invasive plant Ageratina adenophora. Eleven phenolic compounds, including seven new ones, 7-hydroxy-8,9-dehydrothymol 9-O-trans-ferulate (1), 7-hydroxythymol 9-O-trans-ferulate (2), 7,8-dihydroxythymol 9-O-trans-ferulate (3), 7,8-dihydroxythymol 9-O-cis-ferulate (4), methyl (7R)-3-deoxy-4,5-epoxy-D-manno-2-octulosonate 8-O-trans-p-coumarate (5), methyl (7R)-3-deoxy-4,5-epoxy-D-manno-2-octulosonate 8-O-cis-p-coumarate (6), and 3-(2-hydroxyphenyl)propyl methyl malonate (7), were isolated from a bioactive subfraction of the ethanol extract of the roots of A. adenophora. The new structures were established on the basis of detailed spectroscopic analysis. The potential phytotoxic effects of these compounds on the germination of Arabidopsis thaliana seeds were tested by a filter paper assay. Compound 7 and known compounds 3-(2-hydroxyphenyl)-1-propanol (8) and o-coumaric acid (9) remarkably showed inhibition activity against Arabidopsis seed germination at a concentration of 1.0 mM. Compounds 1, 2, 5, 6, and 10 showed slight inhibitory activity at the test concentration after treatment for 3 days, while the other compounds showed no obvious inhibitory effects. Moreover, 7-9 were further found to show obvious inhibitory activity on retarding the seedling growth of Ar. thaliana cultured in soil medium.