Abstract: This article analyzes the three-dimensional structure of Bacillus subtilis protease homology modeling, and compares gene codons with different biological cell vector gene codon preferences, and determines the more consistent expression vector of subtilis protease. The results show that more than 90% of the amino acid residues of the subtilis protease three-dimensional prediction model fall in the optimal region, which is a high-quality prediction model, and its main structure is α-helix and irregular structure. Comparing the Bacillus subtilis protease gene with the cell vector genomes of different candidate organisms, it is found that Pichia pastoris is the most suitable expression vector for the subtilis protease.