Patients with ulcerative colitis (UC) often exhibit affective disorders, such as depression and anxiety. The underlying neurological mechanisms of these symptoms, however, remain poorly understood. This study aimed to explore alterations in functional connectivity (FC) both within and between resting-state networks (RSNs) in individuals with ulcerative colitis. Twelve meaningful RSNs were identified from 22 ulcerative colitis patients and 23 healthy controls using independent component analysis of functional magnetic resonance imaging data. Correlation analyses were performed between clinical indices, neuropsychological assessments and neuroimaging data. Compared with healthy controls, UC patients showed increased intranetwork FC, mainly located in the right temporal pole, orbitofrontal cortex, and left superior temporal and Rolandic opercular cortices within the auditory network. Increased intranetwork FC in the Rolandic opercular cortex was also observed in UC patients during remission phase, while no significant alterations were detected in patients with active-phase UC. In addition, UC patients exhibited increased connectivity between the dorsal attention and the left frontoparietal network, as well as between the anterior default mode network and the posterior default mode network, with distinct patterns of internetwork connectivity observed across different clinical phases. No significant correlations were found between altered brain regions and psychological scales in UC patients. These findings imply that UC patients may undergo functional network alterations, affecting both intranetwork connectivity within RSNs and internetwork connectivity between RSNs.