Abstract: Two biological agents, EM and TRI, were applied in soil on a continuous cropping field of Panax notoginseng to study the remediating effect on the soil and the mechanism associated with the application. Treatments with the agents were found significantly increased the seedling emergence rate and survival rate as well as the root yield. All nutrients in the soil treated with EM were increased, while the available potassium in the soil treated with TRI significantly improved. The HPLC analysis showed no accumulation of phenolic acids in the rhizosphere soil by these treatments indicating that allelochemicals were not directly, but might indirectly, involved in the detrimental effect on P. notoginseng caused by continuous cropping. The DGGE and qRT-PCR test results showed that both EM and TRI, especially TRI, could increase the population of beneficial, while depressed the harmful, bacteria in the soil. Thereby, the rhizosphere soil was effectively repaired by alleviating the deficiency brought about by the continuous cropping practice, and consequently, the growth and yield of P. notoginseng was significantly recovered or improved.