To study the relationship between the disease resistance of Radix Aconiti Lateralis Praeparata and the diversity of fungi system under the guidance of systematic theory of Chinese herbal medicine. Methods:High-throughput technology was used to build the rhizoplane fungus library of different types of Radix Aconiti Lateralis Praeparata, and then the relationship between the diversity index and the anti-disease capacity was analyzed. Results:There were differences in the dominant strains and the diversity of fungi community for the rhizoplane soils between the Xiao-Hua Radix Aconiti Lateralis Praeparata and the Gua-Ye Radix Aconiti Lateralis Praeparata, the healthy and pathogenic Radix Aconiti Lateralis Praeparata; The root system of Radix Aconiti Lateralis Praeparata affect the structure of soil fungi. Atheli arolfsii，Mucor racemosus were the pathogenic fungi, while the Mortierella, Penicillium are antagonistic fungi to root rot pathogens. Conclusion:The results provide theoretical guidance for good quality management of Radix Aconiti Lateralis Praeparata agriculture, and enrich the theory and analysis methods for the system science of Chinese herbal medicine.