The loss of red hue in dry red wine has been a persistent issue for wine enterprises in western China. We investigated the changes in anthocyanins and non-anthocyanin phenols during the industrial-scale fermentation and one-year bottle aging of Vitis vinifera L. Merlot and Vitis vinifera L. Marselan, respectively, using the grapes in the Ningxia region. We also examined their correlation with color characterization. The study found that both anthocyanins and non-anthocyanin phenolics were rapidly extracted from grapes during alcohol fermentation. However, their concentrations decreased rapidly during malolactic fermentation. On the other hand, Vitisin A and Vitisin B were formed during alcoholic fermentation and decreased slowly from malolactic fermentation to storage period. Directly polymerized pigments (F-A and A-F), bridged polymerized pigments (A-e-F), and flavanyl-pyranoanthocyanins (A-v-F) from the reactions of anthocyanins (A) and flavan-3-ols (F), as well as pinotins were generated during the later stages of alcoholic fermentation, and remained at a high level throughout malolactic fermentation and bottle storage. Partial least squares regression and Pearson correlation analyses revealed that the red hue (a* value) of ‘Merlot’ and ‘Marselan’ wines was closely associated with monomeric anthocyanins and F-A type pigments. Furthermore, four pinotin components were positively correlated with the red hue (a* value) of ‘Merlot’ wine. These primary red components of the two varieties had a positive correlation with the level of flavan-3-ols. The data suggest that elevating the flavan-3-ol concentration during fermentation aids in improving the color stability of red wine.