Many crops suffer from the replant problem in the modern cropping system, and the root-associated microbiome is important for the health of plants, especially in the consecutive monocropping system. In our study, we measured microbial population changes under a consecutive monoculture system of Pseudostellaria heterophylla and interaction between phenolic acids in root exudates and typical pathogen and beneficial bacteria. The results illustrated that successive cropping of P. heterophylla shifts the diversity and structure of microbial community in rhizosphere soil. The diversity of microbial community in rhizosphere soil of P. heterophylla was decreased with the increase of planting years while the structure of the microbial community deteriorated. Moreover, the numbers of typical pathogens increased and the amount of beneficial bacteria decreased with the increasing years of monoculture. These changes finally resulted in a microecology imbalance in P. heterophylla rhizosphere and caused more and more serious consecutive monoculture problems in the long run. Further study revealed that phenolic acids in the root secretion of P. heterophylla increased over time, which was closely related to changes in rhizospheric microorganisms. In conclusion, our research reveals that under consecutive monoculture system of P. heterophylla, allelopathic substances such as phenolic acids secreted by roots accumulate increasingly and they can mediate the changes of microbial community structure, which result in the changes of rhizosphere microbiomes of P. heterophylla with the phenomena of fewer beneficial microorganisms and more pathogenic microorganisms. Finally, a large number of pathogenic microorganisms cause severe disease. Adding the beneficial microbiomes into rhizosphere of P. heterophylla can alter the rhizosphere microbiome inducing the beneficial microbiome to become the dominant population which alleviates the replant disease. The result provides a new avenue for modulating the root microbiome to enhance crop production and sustainability, especially in the monoculture system.