BackgroundInflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn’s disease (CD), is a chronic, progressive, and recurrent intestinal condition that poses a significant global health burden. The high prevalence of neuropsychiatric comorbidities in IBD necessitates the development of targeted management strategies.MethodsLeveraging genetic data from genome-wide association studies and Immunochip genotype analyses of nearly 150,000 individuals, we conducted a two-sample Mendelian randomization study to elucidate the driving force of IBD, UC, and CD on cortical reshaping. Genetic variants mediating the causality were collected to disclose the biological pathways linking intestinal inflammation to brain dysfunction.ResultsHere, 115, 69, and 98 instrumental variables genetically predicted IBD, UC, and CD. We found that CD significantly decreased the surface area of the temporal pole gyrus (β = −0.946 mm2, P = 0.005, false discovery rate-P = 0.085). Additionally, we identified suggestive variations in cortical surface area and thickness induced by exposure across eight functional gyri. The top 10 variant-matched genes were STAT3, FOS, NFKB1, JAK2, STAT4, TYK2, SMAD3, IL12B, MYC, and CCL2, which are interconnected in the interaction network and play a role in inflammatory and immune processes.ConclusionWe explore the causality between intestinal inflammation and altered cortical morphology. It is likely that neuroinflammation-induced damage, impaired neurological function, and persistent nociceptive input lead to morphological changes in the cerebral cortex, which may trigger neuropsychiatric disorders.