Abstract: Soil-borne diseases have become a major factor limiting the improvement of crop yield and quality because of their wide distribution, rapid spread, and server harmfulness. In recent years, advances in multi-omics technologies have shed light on the changes of soil microbial community structure and function under rational application of organic fertilizers, as well as their mechanisms of inhibiting soil-borne diseases. These insights are of great significance to reduce chemical fertilizers and pesticides application and promote the agricultural green development. This paper reviewed the prevention and control effects of organic fertilizer application on soil borne diseases, analyzed the structural and functional responses of rhizosphere microorganisms in regulating soil borne diseases under such conditions, and described the soil driving factors of regulating rhizosphere microorganisms. Furthermore, the inhibition mechanisms related to rhizosphere microorganisms on soil-borne disease were summarized from the aspects such as the direct effects of rhizosphere soil microorganisms, soil microbial interactions, and induction of plant immunity. The article also discusses and outlines key future research directions on the impact of rational application of organic fertilizers on soil-borne diseases, aiming to regulate soil microbial diversity and stability through fertilization management, thereby promoting soil and plant health.