The invention discloses a trehalose synthase mutant and a preparation method and application thereof and belongs to the field of genetic engineering and enzyme engineering. The 271st Gln codon near the active center of trehalose synthase of trehalose synthase of Thermobifida fusca YX is converted into the Met codon, the 220th Ile codon is converted into the Val codon, the 228th Val codon is converted into the Ile codon, the 290th Cys codon is converted into Val codon, the 294th Phe codon is converted into the Tyr codon, and the 332nd Ile codon is converted into the Phe codon, so as to respectively obtain mutants Q271M, I220V, V228I, C290V, F294T and I332F. Based on the I220V, amphimutation is carried out to obtain mutants I220V / Q271M, I220V / V228I, I220V / C290V, I220V / F294Y and I220V / I332F. The mutants can be used for improving the trehalose conversion rate prepared by trehalose synthase and have relatively high industrial value.