With increasing emphasis on potato production, the planting scale and professional degree of potato grow very fast in recent years in China. However, ever-increasing application intensity of chemical fertilizers and pesticides, together with succession cropping, leads to more and more serious soil-borne diseases representing by potato common scab. In some areas, the incidence of soil-borne diseases even reaches 90% causing huge economic loss to farmers. [Objective] To monitor the changes of soil bacterial population due to different planting patterns and intensities of fertilization, analyze the relationship between occurrence of soil-borne diseases and change of soil-environment, provide theoretical basis for effectively controlling soil-borne diseases of potato. [Methods] Soil rhizosphere samples were collected from three distinct potato fields continuously cropped for one-year in Xiji (Ningxia, northwest), three-year in Guyuan (Hebei, north) and five-year in Hailar (Inner Mongolia, northeast) with low, high and rare incidence, respectively, of soil borne diseases. Then, high-throughput sequencing technology was used to comparably analyze the bacterial community structure and diversity of these samples. [Results] A total of 617558 effective reads and 3077 sortable operating units (OTUs) were obtained from the 3 groups of samples. Among them, the dominant component was Proteobacteria with a proportion over 33%. Compared with the soil samples from the field without occurrence of potato soil-borne diseases, the bacterial abundance and diversity decreased significantly in the soil samples from the field with high incidence of potato soil-borne diseases. Meanwhile, augmentation and reduction of the relative abundance of pathogenic and probiotic bacteria, respectively, also were observed. Specifically, we found the relative abundance of Actinobacteria increased on a large scale, whereas that of Proteobacteria, Chloroflexi and Acidobacteria decreased dramatically. Moreover, we found that composition changes and quantities of some bacteria (especially Actinomycetes) were closely related to the total phosphorus content of soil. [Conclusion] Excessive application of chemical fertilizers and perennial continuous cropping affected the soil bacterial community and damaged soil ecological environment thus resulting in potato soil-borne diseases eventually. In addition, phosphorus content change may be one of the important factors that alter community structure of soil microbes.