The paper aims to effectively take advantage of the merits of Cabernet Sauvignon and Merlot clonal lines, and provide basis for breeding of new wine grape varieties of higher polyphenol content. The author used four clonal lines of Cabernet Sauvignon and Merlot as materials, measured flesh berry mass, soluble solid content (TSS) and titratable acid content, evaluated total anthocyanins content in pericarp, total polyphenol, tannin, total flavonoid and proanthocyanidin in pericarp, flesh and seed with colorimetric method. The results showed that there was no significant difference in single fruit weight of four clonal lines of Cabernet Sauvignon (CS) and Merlot (M). Among the four Cabernet Sauvignon clones, the TSS of CS170 and CS338 was the highest and the lowest respectively, however, the titratable acid content of CS338 and CS685 was the highest and the lowest respectively. While among the four Merlot clonal lines, the titratable acid content of M181 and M346 was the lowest and the highest respectively. Obvious difference was observed in the polyphenol content of pericarp, flesh and seed in different clonal lines. CS338 had the highest total phenol, tannin, total flavonoids and proanthocyanins in pericarp, while CS169 had the highest content of those in seeds; M348 had the highest total phenol, tannin and anthocyanins in pericarp, while M181 had the highest total phenol and tannin in seeds. There were fruit quality differences among varieties of Cabernet Sauvignon and Merlot, and differences among different clonal lines. The phenolics content in the pericarp was higher, while that in the flesh was the lowest. The pericarp of CS338 and seeds of CS169 had the highest total phenol, tannin, total flavonoids and proanthocyanins; while the total phenol, tannin and anthocyanins in pericarp of M348 was the highest, M181 had the highest total phenol and tannin in seeds.