Abstract: Bioinformatics was used to analyze the sequence of potassium channel proteins in fungi,so as to infer and predict its structure and function. This paper screened the saccharomy cescerevisiae,Aspergillus flavus,A. fumigatus,Fusarium graminearum,A. flavus,Phycomyces blakesleeanus 12 kinds of fungi of the potassium ion channel proteins,such as combination Blast,ProtParam,SignalP and Swiss-Model of bioinformatics website and software for the physical and chemical properties of these proteins,system evolution,the structure and function of protein domain were analyzed. The results showed that the amino acid sequence length of the selected potassium channel protein was between 659~928 aa,and the theoretical equivalence point was between 5.45~9.54,mainly located in the plasma membrane and vacuole. Secondary structure analysis showed that fungus potassium ion channel proteins were by alpha-helix,beta-folding,no rules curly and chain extension structure components,such as highly similar,its spatial structure and 12 kinds of potassium ion channel proteins had a conservative TxGYGD potassium characteristic fragment ions selectors.