Abstract: As one of the most destructive phytopathogenic fungi in the world, Fusarium spp. encompasses a wide variety of species capable of infecting numerous crops and causing diseases such as wilt, root rot, and Fusarium head blight. These diseases pose a formidable threat to the growth of crops, resulting in substantial damage to both yield and quality. Although traditional chemical control can manage plant diseases, the long-term use of chemical fungicides readily induces drug resistance in pathogens and causes serious harm to the ecological environment. Therefore, there is an urgent need for the development of environmentally friendly and highly efficient biological control strategies. In plants, the rhizosphere microbiome, often regarded as the plant’s “second genome”, forms a biological barrier in the rhizosphere to suppress the occurrence of plant diseases and plays a vital role in maintaining plant health. The mechanisms underlying this protection include competition between rhizosphere microorganisms and Fusarium for limited soil nutrients, the secretion of secondary metabolites that directly Fusarium growth, and the modulation of plant hormonal balance, which trigger systemic resistance in plants. In recent years, the advances of bioinformatics technology have significantly enhanced our understanding of the rhizosphere microbiome, particularly in elucidating the interaction mechanisms among pathogen, plant, and microorganisms. It has become a hotspot and frontier in the development and innovation of biological agents. Based on this, this paper introduces the pathogenic process of Fusarium, summarize the research progress in using rhizosphere microorganisms to resist Fusarium diseases, and analyzes the mechanism of using synthetic microbial communities to combat Fusarium diseases, and explores their advantages and potential application values. The aim is to provide solutions and strategies for the development of green disease prevention and control, especially the development of green biological control agents, thereby promoting the green development of agriculture.