In this study, we generated a mutant population of tartary buckwheat cultivar 'Chuanqiao 2' treated by 50 mmol ethyl methanesulfonate (EMS) solution. We recorded the phenotypic variations of M2 to M3 lines, and also measured the content of chlorophyll and anthocyanin in the mutant plants with leaf and stem color variation in the M3 population as well as the transcription level of flavonoid synthesis and metabolite related genes (CHS, F3H, F3'H, FLS and UFGT). 177 mutant plants showing alternations on stem and/or leaf morphology and/or growth stages were found in M2 population with a mutation rate of 10.56%. 665 mutant plants in M3 population were found, including leaves, growth stages, stems, and other types of mutant plants, accounting for 45.86% of the M3 population. We also observed that the shape, color and size of grains in M3 generation changed in varying degrees. We found that the change trend of chlorophyll and anthocyanin content in plants with color variation were almost the same, the content of the red plant at the base of the leaf was higher than that of the normal plant, and the content of the other types of mutant plants were lower than that of the normal plant. Among them, the yellow-green spotted leaf had the lowest content. We also found that CHS and F3H genes had the highest expression level in red stem plants, the FLS genes had the highest expression level in yellow leaf plants, and the expression of F3'H was higher in the two types of plants with red leaf than the other types, and the content was the highest in the plants with the leaf edge turned red. It is speculated that leaf and stem color variations in the M3 population may be contributed by the expression of flavonoid synthesis-related genes. Collectively, these mutants gained from this study provided the basic material for future deciphering the rutin metabolism mechanism.