The first development method of brewery shochu yeast focusing on chromosomal aneuploidy is reported in this study. Euploidy diploid shochu yeast S-3 was treated with a microtubule inhibitor, nocodazole, for the purpose of inducing aneuploidy. Next, 2,3,5-triphenyl tetrazolium chloride (TTC) staining and the growth rate were investigated to select aneuploids. Aneuploids were selected at a frequency of 8.2 × 10−4, which was significantly higher than that of the control group, mainly at chromosomes I, II, III, IX, XII, XIII, and XVI. The acquired aneuploids were evaluated for their metabolic and brewing characteristics. A hierarchical cluster analysis based on endogenous metabolite data discriminated euploid S-3 and aneuploids. In addition, principal-component analysis of the constituents of the broth brewed with the strains discriminated between euploid S-3 and aneuploids. Sensory evaluation of the broth brewed with euploid S-3 and aneuploids showed that it tended to differ in aroma and taste. Specific ethanol production rates of the aneuploids were not deteriorated. The method of this selection made it possible to efficiently obtain aneuploids with various brewing characteristics from brewer’s yeast, which do not correspond to genetically modified organisms. This novel breeding method focusing on chromosomal aneuploidy will facilitate the development of novel shochu yeast strains.