Background We aimed to explore changes in decision-related brain microstructure, brain functional activities, and functional connectivity, and their correlations with cognitive function in end-stage kidney disease (ESKD) patients undergoing peritoneal dialysis (PD). Furthermore, the impact of dialysis on these changes was examined. Methods Thirty ESKD patients undergoing PD, 20 predialysis patients with chronic kidney disease (CKD) stage 5 (predialysis CKD stage 5), and 30 healthy controls (HC) were recruited in this study. Various assessments have been conducted, including neuropsychological scale testing, decision-related behavioral tests, and structural and functional magnetic resonance imaging (MRI) scans. Results Compared to the HC group, PD and predialysis patients performed poorly in the neuropsychology and Iowa Gambling Task (IGT), PD patients showed decreased functional activation and gray matter volume in multiple decision-related brain areas, including the ventromedial prefrontal cortex (vmPFC), orbitofrontal cortex (OFC), and anterior cingulate cortex (ACC) The default mode network (DMN) and salience network (SAN) were the main brain regions with decreased functional connectivity to vmPFC and ACC. Additionally, compared to the predialysis group, PD patients showed enhanced brain activation in decision-related brain regions such as the ACC, vmPFC, and insula. The structure and function variabilities of the vmPFC were correlated with IGT and Montreal Cognitive Assessment score, and the activation of OFC was negatively associated with blood creatinine, cystatin, and parathyroid hormone levels. Conclusion In summary, PD can change the structure and function of decision-related brain circuits (vmPFC-OFC-ACC) and reduce integration within DMN and SAN, which is correlated with cognitive function and clinical features. These suggest that PD can improve patients' cognitive function and disease progression to a certain extent. Keywords: Chronic kidney failure, Cognition, Magnetic resonance imaging, Peritoneal dialysis