Carotenoids are the colored compounds that prominently occur in fruits, vegetables, flowers, algae, fungi, yeast, and marine organisms. The coloration of carotenoids is mainly due to varieties of conjugated double bonds, which act as a light-absorbing chromophores. β-Carotene, α-Carotene, Lycopene, Astaxanthin, Lutein, Zeaxanthin, β-Cryptoxanthin, α-Cryptoxanthin, γ-Carotene and Fucoxanthin are the common carotenoids of the human diet. This review aimed at providing scientific evidence supporting the benefits of nutritional carotenoid intake on gut microbiota modulation in different disease models. Carotenoids have some beneficial effects on human health, and it is due to the activity of pro-vitamin A and antioxidant function. Although mechanisms are under investigation, studies suggest that carotenoid intake may reduce the risk of cancer, cardiovascular disease, eye disease, haematological disease, immune stimulants, and improve cognitive function. Recent studies have shown that carotenoids can modulate gut microbiota composition associated with host health. The human gut harbors a complex community of over 100 trillion microbial cells, influencing human physiology, metabolism, nutrition, and immune function. The combination of extrinsic (lifestyle and medication) and intrinsic (host genetics, immune and metabolic regulations) factors shapes the gut microbiota. Diet is a crucial modifiable factor influencing gut microbiota composition, indicating the potential for therapeutic dietary strategies to manipulate microbial diversity, design, and stability.