Ulcerative colitis (UC), an inflammatory bowel disease (IBD) linked to colon cancer, needs effective natural preventive and therapeutic strategies to alleviate its clinical course. This study investigated the combined effects of phlorotannins (TAs) isolated from Eisenia bicyclis (E. bicyclis) and Lactobacillus casei (LC) on inflammatory markers in UC, with a focus on the aryl hydrocarbon receptor (AhR) axis. In vitro experiments revealed anti-inflammatory effects of the phlorotannin fraction isolated from E. bicyclis, especially in synergy with LC. In vivo experiments showed that a synbiotic combination of TAs and LC mitigated DSS-induced colitis and reduced intestinal shortening and splenic hypertrophy. The TA and LC combination suppressed inflammatory factors (IL-6, TNF-α, Lipocalin 2), while activating tight junction genes (Muc2, Zo-1, Occludin, and Claudin1) and enhancing antioxidant capacity (Nrf2 and Nqo1 genes). Activation of the AhR pathway, which is crucial for regulating intestinal inflammation via IL-22, was evident with both phlorotannin alone and synbiotic administration. The combination of TAs and LC amplified the synergistic effect on intestinal immunity and microbiota, favoring beneficial species and optimizing the Firmicutes/Bacteroidetes ratio. Overall, synbiotic use demonstrated superior preventive effects against UC, suggesting its potential benefits for improving the gut immune system through gut microbiota-derived metabolites.