The invention relates to a method for producing fumagillin by aspergillus fumigatus. The method comprises the following steps: inoculating aspergillus fumigatus into a GMM solid medium to activate strains, wherein the pH value of the GMM medium is 5 to 7; preparing activated strain spores into spore suspension, and then inoculating the spore suspension into a CYA solid medium, a CXMA solid medium or an LMM liquid medium, wherein the pH values of the CYA solid medium and the CXMA solid medium are natural, and the pH value of the LMM liquid medium is adjusted to be 5 to 7, and carrying out culturing at the temperature of 25 to 37 DEG C; collecting cultured aspergillus fumigatus to extract fumagillin and fumagillin derivatives. According to the invention, carbon and nitrogen sources and trace elements of fumagillin which affect the growth of aspergillus fumigatus are aimed to be screened, and the concentration of corresponding trace elements is optimized to obtain higher yield of fumagillin.