Rice-Tartary buckwheat (RTB) is a special germplasm of Tartary buckwheat. In this study, the appraisal of taste quality between RTB and conventional Tartary buckwheat (CTB) was presented, and the metabolites in kernels at three typical grain filling stage (GFS) were investigated. Unlike CTB, RTB showed thin shell seeds without longitudinal furrows at maturity, which was easily artificially dehulled. Sense organ test indicated that RTB exhibited better taste quality because of the higher values of appearance, viscosity, taste and summary were appraised. In total, 92 metabolites were identified in kernels using GM-MS metabolomics platform. The levels of most metabolites changed greatly during grain filling and a large numbers of metabolite-metabolite correlations were found by Pearson correlation coefficient analysis. ANOVA analysis identified 61 differentially expressed metabolites between RTB and CTB, while Venn diagram analysis screened 35 common differential metabolites. Compared with CTB, RTB showed similar levels of lysine and methionine, indicated that RTB own excellent nutritional value. Additionally, RTB exhibited significantly up-regulated levels of most sweeteners (sugars and polyols), which might contribute to better taste. This work provides the first comprehensive metabolomics analysis of kernels between RTB and CTB, which may potentially provide theoretical basis for further research.