Brain iron deposition is correlated with minimal hepatic encephalopathy (MHE). This study aimed to investigate the pattern of altered iron distribution, using quantitative susceptibility mapping (QSM), and to clarify the relationship between iron deposition and neurocognitive changes in MHE. We enrolled 32 cirrhotic patients without MHE (NHE), 21 cirrhotic patients with MHE, and 24 healthy controls, and used the Psychometric Hepatic Encephalopathy Score (PHES) to assess neurocognitive function. All participants underwent magnetic resonance scans with a gradient-echo sequence reconstructing for QSM. We performed voxel-wise and region-of-interest (ROI)-wise analyses to investigate the QSM difference across three groups and to examine the relationship between susceptibility value and PHES. MHE patients exhibited increased susceptibility value in widespread brain areas (family-wise error (FWE)-corrected P < 0.05), which was located mainly in cognition-related regions (such as the prefrontal lobe, precuneus, inferior parietal lobule, insula, thalamus, and superior longitudinal fasciculus), sensorimotor regions (such as the precentral/postcentral gyrus, superior parietal lobule, and posterior corona radiata), visual regions (such as the occipital cortex and posterior thalamic radiation), and auditory regions (such as the temporal lobe). NHE patients also followed a trend of increasing susceptibility in the scattered brain regions, but which did not reach statistical significance (FWE-corrected P > 0.05). We observed negative correlations between cirrhotic patients' PHES and regional susceptibility values (FWE-corrected P < 0.05). Brain iron accumulation (measured using QSM) contributes to cognitive impairments in MHE patients. QSM could provide new insights into the pathogenesis of MHE and facilitate monitoring disease development.