The invention relates to phytopathology, in particular to cotton fungal endophyte CEF-082 and an application of the cotton fungal endophyte CEF-082 in prevention and treatment of cotton verticillium wilt. The preservation serial number of the cotton fungal endophyte CEF-082 is CGMCCNo.11313; the suppression rate of the metabolite of the CEF-082 to colony growth of the cotton verticillium wilt reaches 100%, and the suppression rate to the conidium yield is 70.73%. Greenhouse experimental results show that cotton is pre-inoculated through CEF-082 culture filtrate when true leaves of cotton seedlings appear for the first time, and the control effect on the cotton verticillium wilt is 62.37%; the corn sand grain culture of the CEF-082 is connected into a matrix at the percentage of 2%, and then the cotton seedlings are cultivated, so that the control effect on the cotton verticillium wilt is 66.88%. Compared with bacillus subtilis which is greatly used in production, the control effect is increased by 30.7% on average; the expressions of defense related genes beta-1,3-glucanase, POD, PPO, PAL and the like are improved by inoculating the cotton through the CEF-082, hence, the resistance of plants to the cotton verticillium wilt is enhanced, and the damage of pathogenic bacteria is reduced.