The advance of the grape harvest caused by global warming has to some extent resulted in poor or unstable wine color, this study investigated the potential benefits of grape seeds on wine color to mitigate this negative effect. Anthocyanins and their derivatives, and chromatic characteristics were measured by targeted UHPLC-QqQ-MS/MS and CIELab methods, respectively. The addition of seeds was beneficial to the formation of polymeric pigments and flavanyl-pyranoanthocyanins, while decreased the accumulation of other yranoanthocyanins, monomeric anthocyanins, and acylated anthocyanins during fermentation. All pigment levels in seed wine can be better maintained over time. Compared with the removal of seeds during fermentation, the addition of seeds significantly enhanced the color intensity, bluish hues, and Chroma, while an appropriate amount of seeds favored wine red hue. PLSR showed that the addition/removal of seeds during fermentation could alter red wine chromatic characteristics via modulating anthocyanin profiles. These results can be used as reference to further explore the technological applications of seeds during fermentation for optimizing the potential benefits on red wine color.