•Relationship between secondary metabolites and morphological variations.•40 Cultivars of tartary buckwheat seeds from different regions.•Targeted metabolomics of flavonoids and anthraquinones.•Groats and hulls of tartary buckwheat seeds were studied respectively. Polyphenols (flavonoids and anthraquinones) are one of the most important phytochemicals in Fagopyrum tataricum L. Gaertn. (tartary buckwheat). However, the relationship between the polyphenols of tartary buckwheat seeds and their morphological variations is unclear. We developed a liquid chromatography–mass spectrometry-based targeted metabolomics method to study the chemical profiles of 60 flavonoids and 11 anthraquinones in 40 seed cultivars (groats and hulls). Both flavonoids and anthraquinones were related to variations in seed color; the fold change from yellowish-brown to black seeds was 1.24–1.55 in groats and 0.26–0.76 in hulls. Only flavonoids contributed to significant differences in seed shape; the fold change from long to short seeds was 1.29–1.78 in groats and 1.39–1.44 in hulls. Some differential metabolites were identified at higher concentrations in hulls than in groats. This study provides new insights into differences in polyphenols among tartary buckwheat seeds with different color and shape.