PurposeThis work integrated field investigation results with laboratory experiments to investigate the interaction of rhizosphere soil microorganisms in the continuous cropping of Panax notoginseng and saponins, providing a scientific foundation for overcoming P. notoginseng continuous cropping obstacles.MethodsThe concentrations of saponins were measured using UPLC-MS/MS, and the microbes in the P. notoginseng rhizosphere soil were sequenced using the Illumina MiSeq high-throughput platform.ResultsThe concentrations of ginsenoside Rd, ginsenoside Rg(2), ginsenoside Rg(1), ginsenoside Re, ginsenoside Rb-1 and notoginsenoside R-1 in the rhizospheric soil of infected P. notoginseng increased considerably. The P. notoginseng rhizospheric soil rapidly degraded saponins in the following order: ginsenoside Rd > ginsenoside Rg(1) > notoginsenoside R-1 > ginsenoside Re > ginsenoside Rg(2) > ginsenoside Rb-1. Saponins substantially enhanced the fungal Chao1 index, and Rd had the greatest effect. Saponins shifted the microbial community architecture and abundance in the rhizosphere soil. Ginsenoside Re stimulated the growth of Rhodotorula and Alternaria, ginsenoside Rg(1) significantly increased the production of Spizellomyces, ginsenoside Rd promoted the proliferation of Aureobasidium, and notoginsenoside R-1 fostered the growth of Alternaria. Further investigations showed that increases in Plectosphaerella and Clonostachys were directly and positively related to notoginsenoside R-1, ginsenoside Rg(1), and ginsenoside Rb-1, while an increase in Ilyonectria was strongly and positively related to ginsenoside Rb-1 and ginsenoside Rg(2).ConclusionsThe six saponins have the potential to shape the structure of the microbial community of the P. notoginseng rhizospheric soil, and enrichment in particular saponins lays the foundation for the emergence and proliferation of pathogenic fungi.