Autotoxicity has been considered as one of the critical factors resulting in replanting failure in agriculture. To clarify the chemical reasons for the replanting problems of Pinellia ternate, a widely used and cultivated Traditional Chinese Medicine, eight compounds were isolated and identified from its rhizosphere soil. Bioassays showed that chrysophanol (1), benzofuran (6) and protocatechuic aldehyde (8) obviously inhibited the seedling growth of P. ternate and Raphanus sativus in a concentration-dependent manner. The isolated compounds were further confirmed and quantified by HPLC in the rhizosphere soil and tissues of P. ternate, and the origins of the allelochemicals being released into the soil environment were also investigated. Physiological analyses demonstrated that the allelochemicals evidently affected the levels of protective enzymes in the tested plant seedlings and caused membrane damage, which resulted in the reduction of cell vitality. These findings provide allelopathic evidence for the replanting problems of P. ternate and would be helpful for assessing plant-soil interactions.