Abstract Inflammatory bowel disease (IBD), with its colonic predilection, was frequently complicated by neuropsychiatric comorbidities such as anxiety and depression. To address this, we developed a colon-targeted, prebiotic-based synergistic therapeutic system. This system integrated anti-inflammatory and antioxidative rod-shaped Mn2(Olsa) metal-organic framework (MOF) particles with a yeast β-glucan/konjac glucomannan (YG/KGM) composite gel designed to remodel the gut microenvironment. The resulting Mn2(Olsa)/Gel composite ensured sustained intestinal adhesion and retention, facilitating efficient colon-targeted delivery. It effectively alleviated hallmark pathologies of IBD, including intestinal inflammation, microbial dysbiosis, barrier disruption, oxidative stress, and immune imbalance. In addition, the treatment significantly mitigated IBD associated anxiety- and depression-like behaviors. This work establishes a novel, targeted paradigm for the combined management of IBD and its neuropsychiatric comorbidities.