To investigate the differences and shifts in the content and accumulation of saponins in the taproots of Sanqi ginseng (Panax notoginseng) from different producing areas, and to analyze the relationship between saponins content and accumulation and the quantity of soil-borne fungal pathogens. Sanqi ginseng planting bases established in the traditional producing area (Qiubei, Wenshan) and the emerging producing area (Shilin, Kunming) were chosen, and samples of Sanqi plant and corresponding rhizosphere soil at the two-year seedling stage, two-year root growth stage, three-year flowering stage, and three-year harvesting stage were collected. High-performance liquid chromatography (HPLC) and real-time quantitative PCR were employed to analyze the content of major saponins (R1, Rg1, Rb1, and Rd), as well as the quantity of soil-borne fungal pathogens (Fusarium oxysporum, F. solani, and Cylindrospora destructus). Additionally, the aboveground biomass and belowground biomass of Sanqi ginseng were also measured. Results indicated that producing area had significant effects on the biomass accumulation of Sanqi ginseng. At the three-year harvesting stage, the total fresh biomass and dry biomass of Sanqi ginseng derived from Qiubei were 27.7% and 31.1% higher than those of Shilin. Similarly, producing area also had significant impacts on the content and accumulation saponins in the taproots of Sanqi ginseng, with the level of saponin monomers, total saponin content and accumulation in the Sanqi ginseng from Qiubei being higher than those from Shilin. In particular, the total saponin accumulation in the taproot of Sanqi ginseng at the three-year harvesting stage in Qiubei reached 2364.8 mg, which was 1.56 times higher than those in Shilin. Throughout the entire growth cycle of Sanqi ginseng, the quantity of F. solani and its proportion in fungi in the rhizosphere soils of Sanqi ginseng from Qiubei were significantly (P < 0.05) higher than Shilin, while the quantities and proportions of F. oxysporum and C. destructus were varied. Correlation analysis showed that the quantity and proportion of F. solani in the rhizosphere soil of Sanqi ginseng had significant and positive relationship with the content and accumulation of most saponins in its taproots, except for the two-year seedling stage. Collectively, the results of this study showed that the saponin accumulation of Sanqi ginseng between Qiubei and Shilin was significantly different, and these accumulation differences were closely related to the quantity and proportion of F. solani in the rhizosphere soil. These results provided useful information and scientific basis for deciphering the quality formation mechanism of Sanqi ginseng from the perspective of biological stress and plant-pathogenic microbe interaction.