Three different prebiotics (inulin, fructose-oligosaccharide, and oligo-chitosan) were added to the diets of mice to explore their effects on the digestion and absorption of astaxanthin. The results showed that inulin and oligo-chitosan had no significant effects on the bioaccessibility of algal-derived astaxanthin (p>0.05), whereas fructose-oligosaccharide reduced its bioaccessibility (p<0.01). The bioavailability of algal-derived astaxanthin could be reasonably improved with inulin supplementation. In comparison with the control group, the inulin-treated group showed a significant increase of 36.37% in the area under curve (AUC) of astaxanthin in the liver. The content of short-chain fatty acids (SCFAs) also significantly increased (p<0.05) in the feces of the mice from the inulin-treated group. In particular, the level of acetic acid increased by 139.54% and that of propionic acid increased by 40.04%. 16SrRNA amplicon sequencing results indicated that the relative abundance of Dubosiella and Akkermansia in the insulin-treated group increased by 70.55% and 83.33%, respectively. In conclusion, dietary inulin supplementation may improve the absorption and utilization of algal-derived astaxanthin in the body by changing the composition of intestinal flora. The results of this study highlight a new idea for improving the bioavailability of astaxanthin and provide scientific and technological support for the development of astaxanthin products.