Anthocyanin plays an important role in wine color and quality. The anthocyanin concentration in grapes depends on the variety and is influenced by environmental factors, such as temperature, sunlight, soil, and grapevine practice. In this study, the anthocyanin profiles of two varieties, namely Cabernet Sauvignon and Merlot, from five regions (11 plots) in Xinjiang were examined. The climatic parameters performed noticeable difference between northern and southern of Xinjiang region. Result showed that northern of Xinjiang possessed the relatively lower humidity and higher average temperature in comparison with southern area. In addition, the total anthocyanin profiles of Cabernet sauvignon, which in Changji, Wushitala, Heshuo respectively, were higher than of other plots. This result might be caused by which those have relatively higher altitude than in other plots. For merlot, the higher anthocyanin concentrations performed in southern of Xinjiang, which could be contributed to the lower average temperature and higher relative humidity. Comparing Cabernet sauvignon and Merlot, the latter was easily affected by environment factors, and the anthocyanin composition and concentration of Merlot showed significant differences in different regions.