Carotenoids from different sources have different structures and functions and as a dietary component have potential health benefits for a wide range of organisms. The effects of halophilic Archaea-derived C50 carotenoids on poultry egg quality and gut microbiota remain largely unexplored. In this study, we isolated and obtained a strain of Halalkalicoccus paucihalophilus, named TRM89021, from the Pamir Plateau. It secretes large amounts of carotenoids. We characterized the carotenoid pigments produced by this strain and found that its main components were bacterioruberin and its derivatives. Effects of these carotenoids on egg quality and cecal microbiota composition of hens were investigated. Compared to the BDG, the supplementation with carotenoids in the CDG resulted in significantly lower a* and b* scores at week 5 and a lower b* score and Haugh units at week 2, while egg strength and weight were higher. The CDG also showed increased yolk antioxidant capacity, higher glutathione peroxidase levels, and significantly lower catalase levels (p<0.05). Plasma analysis revealed elevated total bilirubin and aspartate aminotransferase levels, along with reduced inorganic phosphorus levels in the CDG (p<0.05). No significant differences in cecal microbiota diversity were observed between groups at any taxonomic level (p>0.05). This result suggests that halophilic archaea-derived carotenoids display potential to be a natural feed supplement to improve egg quality. Our study provides a theoretical basis for application of archaea-derived carotenoids in poultry diets.