The body color of aquatic products is a key indicator that aquaculture practitioners use to evaluate health status and consumers use to judge quality. Carotenoids are natural pigments that are mainly pigmented compounds responsible for red, yellow, and orange coloration. They have important functions, such as immune and antioxidant modulation. Recently, a novel strain of Pelodiscus sinensis with bright yellow color, named the Yongzhang golden turtle (YGT), was obtained through selective breeding. However, the actions of carotenoids on its coloration, antioxidant activities and immune competence have not been investigated yet. In this study, we examined the concentration of carotenoids in the skin and calipash of the atrovirens wild-type turtle (AWT) and YGT by spectrophotometry and found that the concentration of carotenoids in the YGT was significantly higher than that in the AWT. Then, we measured relevant antioxidant activity indicators, including total antioxidant capacity (T-AOC) and malondialdehyde (MDA), by commercial kits in the YGT and AWT, identifying higher activities of T-AOC in the YGT compared with those in the AWT, while MDA contents were decreased in the YGT compared to those in the AWT. We quantified the immune competence of the YGT and AWT using plasma bacteria-killing ability (BKA) and immunoglobulin M (IgM) expression. Compared to plasma from the AWT, that of the YGT showed higher antibacterial activity against Escherichia coli, Aeromonas hydrophila, Staphylococcus aureus, Salmonella typhimurium, and Citrobacter freundii. However, there was no difference in IgM expression between the YGT and AWT. Correlation analysis suggested that carotenoids concentration were positively associated with T-AOC and BKA, and negatively associated with MDA. In conclusion, the bright yellow color of YGT was mainly caused by carotenoids, which could enhance the antioxidant capacity and immune competence. Therefore, the YGT, with yellow coloration, possesses a high ornamental value and is much better in quality than the AWT.