Fucoxanthin, a carotenoids exclusively derived from algae, exerts its bioactivities with modulation of gut microbiota in mice. However, the mechanisms through which fucoxanthin regulates the gut microbiota and its derived metabolites/metabolism in human remian unclear. This study investigated the effects of fucoxanthin on gut microbiota and metabolism of non-obese individuals using an in-vitro simulated digestion-fermentation cascade model. The results showed that about half of fucoxanthin was not absorbed in the intestine thus reached the colon. The gut microbiota from volunteer feces underwent significant changes after 48 or 72 hour in-vitro fermentation. Specifically, fucoxanthin significantly enhanced the relative abundance of Bacteroidota and Parabacteroides, leading to improved functions of the gut microbiota to the development, glycan biosynthesis and metabolism, digestive system, endocrine system and immune system. Fucoxanthin recovery during fermentation showed a decrease trend with slight bio-conversion of fucoxanthinol. Notably, fucoxanthin supplementation significantly altered the metabolites, especially bile acids and the indoles in the simulated human gut ecosystem. Correlation analysis indicated the involvement of gut microbiota in manipulation of these metabolites by fucoxanthin. Moreover, all these altered metabolites revealed improvement of fucoxanthin capacity in manipulating gut metabolism, especially lipid metabolism. Overall, fucoxanthin determinedly reshaped the gut microbota and metabolism, implying its health benefits potential in non-obese individuals.