To explore the inhibitory effects of Eupatorium adenophorum extracts on weed seed germination and early seedling growth, three common weed species, Echinochloa crusgalli, Chenopodium glaucum, and Amaranthus retroflexus, were chosen as materials to investigate seed germination and seedling growth, morphological characteristics of root tip cells and root border cells(RBCs), and pectin methyl esterase(PME) activities in the root cap using suspension cultures. The results indicated that Eupatorium adenophorum extracts significantly inhibited the seed germination, and damaged the root tips, including swelling, shrinking, and deformation of root tips, loss of epidermal root tip cells, and disordered distribution of internal root tip cells. Moreover, Eupatorium adenophorum extracts obviously inhibited RBC number; the RBC number of the three weed species decreased by 44.5%(E. crusgalli), 48.3%(C. glaucum), and 64.0%(A. retroflexus), respectively, compared with the untreated control). Eupatorium adenophorum extracts also induced RBC apoptosis; the RBC apoptosis rate of the three weed species decreased by 81.7%(E. crusgalli), 91.3%(C. glaucum), and 97.1%(A. retroflexus), respectively, compared with the untreated control. In addition, Eupatorium adenophorum extracts increased the thickness of RBC adhesive layers, and improved PME activity. Taken together, these findings indicate that Eupatorium adenophorum extracts inhibited RBC development and induced RBC apoptosis, thereby weakening the protective effects of RBC on root tips, and eventually inhibiting the growth and development of the whole root system. Our findings shed light on the development of bioherbicides derived from Eupatorium adenophorum extracts.