Caitai (Brassica compestris. var. tsai-tai Hort.) is a non-heading Chinese cabbage variety popular in south China. To meet with market demand, we bred novel purple and green Caitai cultivars, in which leaves, petioles, and stems appeared purple and green, respectively. To study the mechanism of color devlopment in the purple Caitai and green Caitai, the leaves, petioles, and stems from the two Caitai cultivars were harvested, for assessing metabolite levels and gene expression by metabolomics and high throughput sequencing. In total, we obtained 14 differentially accumulated flavonoids in three comparison groups (green leaves versus purple leaves, green petioles versus purple petioles, and green stems versus purple stems), including 10 anthocyanins. The contents of 10 anthocyanins were significantly higher in purple Caitai compared with green Caitai. To study the genes involved in the anthocyanin biosynthesis and accumulation, high throughput sequencing was carried out and revealed 878 up-regulated and 928 down-regulated genes between the three comparison groups. Conjoint analysis revealed that nine structural genes which encode key enzymes involved in anthocyanin biosynthesis, including BraCCoAOMT, BraANS1, BraFLS, BraCHS3, BraF3H1, BraF3H2, BraF3′H, BraLDOX, and BraDFR, were up-regulated in purple Caitai compared with green Caitai. Moreover, the expression of BraFLS, BraLDOX, BraF3H2, and BraCHS2 was further confirmed by qRT-PCR which was consistent with the results from high throughput sequencing. Collectively, our study demonstrated that the up-regulated structural genes promoted anthocyanin biosynthesis and accumulation in purple Caitai, resulting in purple the leaves, petioles, and stems.