The invention relates to microbial fertilizers and particularly relates to a microbial fertilizer for preventing and treating cotton verticillium wilt and a use method thereof. Cotton endophytic fungiCEF08111 is taken as biocontrol bacteria and is fermented with sheep manure to generate the microbial fertilizer, so that the cotton verticillium wilt can be effectively prevented and treated. The biocontrol bacteria in the microbial fertilizer can be uniformly colonized in organic matters, is high in effective concentration and has good prevention and treatment effects; by carrying out a greenhouse seedling stage experiment, the prevention and treatment effects to the cotton verticillium wilt reach 74.1%; and the microbial fertilizer has huge potential to the prevention and treatment of thecotton verticillium wilt, the farmland pollution can be reduced, the soil structure can be improved, the use amount of chemical fertilizers can be reduced, the culturing condition of a biocontrol bacteria strain is simple, the industrial production can be easily realized, and the microbial fertilizer has good development and application prospects.