Patients undergoing cardiopulmonary bypass (CPB) often experience neurological complications, but the neurobiological mechanisms remain unclear. This study combined resting-state fMRI, structural MRI, and cognitive testing to examine brain changes in 124 CPB patients and matched controls. Reduced amplitude of low-frequency fluctuation (ALFF) in the bilateral frontoparietal lobes indicated diminished neural activity among patients, and these ALFF values were positively correlated with the degree of executive dysfunction measured by the attention network test. Functional connectivity within the frontoparietal executive control network was weakened. Brain structural analysis revealed cortical thinning in frontoparietal and temporal regions, increased sulcal depth in medial orbitofrontal areas, and reduced gyrification in the insula suggesting long-term morphological impacts. These findings demonstrate CPB-associated functional and structural alterations in brain regions critical for cognition, providing neuroimaging evidence for postoperative dysfunction and potential neuroprotective strategies.