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The fungal community structure and soil fertility in rhizosphere soil have an important effect on the health of Panax notoginseng (P. notoginseng). The attack of pathogenic fungi and the imbalance of soil fertility can easily lead to diseases. The effect of Bacillus subtilis on improving the community structure of soil fungi has been confirmed, and the corresponding biological agent products have been commercialized. A pot experiment carried out in a greenhouse explored the effect of a biological agent and fertilizer on the fungal community in the rhizosphere of P. notoginseng. In the experiment, fertilization and the addition of biological agents were set up with three gradients, respectively, and the full coupling experiment was adopted, and the blank control group (CK) was set up at the same time. Therefore, there were thirteen treatments in the experiment. NH4 decreased between 36.42% and 11.56%, AP increased between 6.03% and 92.46%, AK increased between 2.99% and 25.40%, TN increased between 0.10% and 9.41%, and TP increased by 18.25% to 47.73% The addition of Bacillus subtilis biological agent decreased the Chao1, Shannon, Simpson, and ACE index of fungi in the rhizosphere soil of P. notoginseng. The Chao1 index decreased between 0.39% and 78.22%; the ACE index decreased between 0.43% and 78.24%. The main pathogenic fungi Cylindrocarpon and Fusarium of P. notoginseng were different in the experimental results. Cylindrocarpon decreased under F1C1, F2C1, and F3C2 treatments, while Fusarium increased under F1C1, F2C2, F3C1, and F3C3 treatments and decreased Fusarium content in rhizosphere soil of P. notoginseng in other treatments. RDA analysis (Redundancy analysis) showed that NH4-N was negatively correlated with the main pathogen Cylindrocarpon, Fusarium, and Ilyonectria, while AP and AK were positively correlated with Cylindrocarpon, Fusarium, and Ilyonectria. The results of the GRA-TOPSIS analysis showed that the score of F3C2 was the highest, while F2C3 and F2C1 ranked second and third, respectively. The calculation results of the theoretical model based on GRA-TOPSIS analysis showed that the GRA-TOPSIS score was highest when the theoretical optimal fertilizer application rate and bacteria application rate were 116.31 kg hm−2 and 15.83 kg hm−2, respectively. [ABSTRACT FROM AUTHOR]