Polyploid plants grow well, are stress tolerant, and are rich in nutrients and bioactive compounds. Thus, they areuseful for improving crop quality and yield. In this study, we compared the seed characteristics and metaboliteprofiles of diploid and tetraploid tartary buckwheat, which was developed via an artificially induced chromosomedoubling event. The length, width, area, and thousand-grain weight were greater for the tetraploid seeds than forthe diploid seeds. However, the germination rate decreased for the tetraploid seeds. Additionally, there was a gapbetween the shell and kernel of the tetraploid seeds. Moreover, the water absorption rate was higher for the tetra-ploid than for the diploid seeds. Chromosome doubling increased the seed totalflavonoid content and deepenedthe seed color. A principal component analysis of the ultrahigh-pressure liquid chromatography-high resolutionmass spectrometry data revealed the clear separation between the diploid and tetraploid samples. An orthogonalpartial least squares-discriminant analysis and other multivariate statistical analyses identified 83 differentiallyabundant compounds, with most of theflavonoid metabolites more abundant in the tetraploid than in the diploidseeds. Research on tartary buckwheat polyploidy may result in enhanced germplasm resources and may clarify themechanism underlying the biosynthesis of bioactive compounds