Crohn's disease (CD) is a chronic nonspecific inflammatory bowel disorder of unknown etiology that may involve any segment of the gastrointestinal tract from the mouth to the anus. Due to its incurability and recurring nature, CD patients often experience psychological comorbidities such as anxiety and depression. The potential link and molecular mechanisms between these psychological issues and disease progression remain unclear. Recent evidence highlights the gut-brain axis as a key factor in CD pathogenesis, but the bidirectional regulatory mechanisms between psychological comorbidities and intestinal inflammation need further study. With the rapid development of multimodal Magnetic resonance imaging (MRI) technologies, significant progress has been made in their application in CD-related neurobiological research. Many studies have found significant structural and functional changes in specific brain regions of CD patients, including reduced gray matter volume (GMV), abnormal functional connectivity (FC), and altered brain metabolism. Of these, alterations in the anterior cingulate cortex, hippocampus, and insula are highly reproducible across different MRI modalities. These findings reveal the potential profound impact of CD-related psychological comorbidities on the brain. This review, based on the regulatory mechanisms of the microbiota-gut-brain (MGB) axis, summarizes the latest applications of MRI technologies in CD involving psychological comorbidities and discusses emerging research directions. It emphasizes the translational potential of neuroimaging in guiding personalized treatment strategies and improving CD patient outcomes. EVIDENCE LEVEL: Level 3. TECHNICAL EFFICACY: Stage 2.