This study aimed to develop a novel astaxanthin nanoparticle using gum arabic (GA) and whey protein powder enriched with milk fat globule membranes (MFGM-WPI) as carriers and to investigate its effect and alleviation mechanism on colitis in mice. We demonstrated that MFGM-GA-astaxanthin could improve the bioaccessibility of astaxanthin and cope with oxidative stress more effectively in a Caco-2 cell model. In vivo studies demonstrated that MFGM-GA-astaxanthin alleviated colitis symptoms and repaired intestinal barrier function by increasing the expression of mucin 2, occludin, and zonula occludens-1. This was attributed to the alleviating effect of MFGM-GA-astaxanthin on oxidative stress. Moreover, MFGM-GA-astaxanthin restored the abnormalities of flora caused by dextran sulfate sodium, including Lactobacillus, Bacteroides, Ruminococcus, and Shigella. This study provides a basis for the therapeutic effect of astaxanthin nanoparticles on colon diseases.