The invention discloses an ITS-RFLP method for rapidly identifying main cotton pathogenic fungus, which mainly comprises the following steps: 1) extracting cotton main pathogenic fungus mycelia genome DNA, which comprises Verticillium dahliae, Verticillium alboatrum, Rhizoctonia solani, Fusarium moniliforme, Trichothecium roseum and Fusarium oxysporum; 2) amplifying ribosome internal transcribed spacer (ITC) using PCR: carrying out rapid amplification using general primer ITS4 and ITS5 of fungi ITS; 3) carrying out enzyme digestion reaction using restriction enzymes and identifying band spectrums: carrying out single digestion reaction of ITS products of cotton main pathogenic fungus randomly using restriction enzymes HhaI, HaeIII, TaqI and Sau3A whose recognition sites are four basic groups, and comparing ITS-RFLP band spectrum correlation tables and standard electronic maps, thereby rapidly identifying classes of pathogens. Compared with traditional time-consuming and labor-consuming morphological and physiological identification as well as ITS clone sequencing identification method of pathogen with high cost, the invention has the advantages of rapid, accuracy and economy, and simultaneous identifications of a plurality of pathogenic fungus.