The invention discloses a seed medium for producing fumagillin by fermentation of Aspergillus fumigatus and its fermentation medium, and also discloses a method for producing fumagillin by fermentation of Aspergillus fumigatus. The Aspergillus fumigatus is inoculated in the seed medium to activate the strain, and the pH value of the medium is natural; step 2, the activated strain is prepared to prepare a monosporous bacteria suspension and inoculate the fermentation medium, and the pH of the fermentation medium is When the value is natural, the fermentation culture is carried out, and the fumagillin in the fermentation broth is collected. The present invention screened the carbon sources affecting fumagillin, and unexpectedly found that the use of glycerol as the carbon source could avoid the production of by-products such as gliotoxin, without the need for subsequent separation and purification, reducing production costs and facilitating large-scale production in factories .