The invention discloses a swine alexin pBD1 polypeptide, an encoding gene thereof and an application thereof to inhibition of swine pathogenetic fungi. The swine alexin pBD1 polypeptide provided by the invention is a protein shown as (1) or (2), wherein (1) is constituted by an amino acid sequence shown as SEQ ID No.2, or (2) is obtained by performing substitution and/or deletion and/or addition of one or more amino acid residues on an amino acid residue sequence shown as a SEQ ID No.2 and have equivalent activity. A polypeptide sequence of swine alexin pBD1 is modified, in-vitro expression is performed by using colon bacillus, a large quantity of bioactive alexins can be obtained at low cost, the problems of difficulty in separating natural alexins and high production cost of a chemical synthetic method are solved, and large-scale production of swine alexins is facilitated. Moreover, the swine alexin pBD1 produced by fermenting still has high bioactivity, and can be used for inhibiting multiple swine pathogenetic fungi.