Twenty-two fungi with whole genome sequence published and the antiSMASH database were used to classify and annotate the gene clusters of synthesizing secondary metabolites of plant pathogenic fungi with different nutritional types in order to clarify the role of secondary metabolites of plant pathogenic fungi with different nutritional types in infecting plants and the differences in gene clusters. The results showed that the type and number of gene clusters of synthesizing secondary metabolites of hemi-biotrophs and necrotrophs fungi were higher than that of biotrophs fungi. The results of further analyzing the gene clusters of synthesizing secondary metabolites of non-ribosomal peptide synthetase,polyketide synthase and terpene showed that the number of NRPS gene clusters,PKS gene clusters and terpene gene clusters in hemi-biotrophs and necrotrophs pathogenic fungi were higher than that in biotrophs pathogenic fungi as well. It will provide an important theoretical basis for further analyzing the function of the gene cluster of synthesizing secondary metabolites of different trophic types of fungi and identifying new drug targets. Analyzing the gene clusters of synthesizing secondary metabolites in fungi and clarifying the differences in gene clusters of synthesizing secondary metabolites of different nutrition types of fungi is conducive to the better development of medicaments for preventing and controlling novel action targets of plant diseases.