Previous neuropsychological studies have demonstrated that liver transplantation (LT) is an effective method for improving the cognitive function of cirrhotic patients. However, the neural basis underlying the effects of LT is still unclear. Neuroimaging studies investigating changes in brain structures or functional networks mainly focus on patients without overt hepatic encephalopathy (HE). In this study, we recruited patients with and without overt HE and studied alterations in resting-state brain activity by quantizing the amplitude of low-frequency fluctuation (ALFF) before and 1 month after LT to study the short-term effect of LT in each group. Neuropsychological analyses indicated significant improvement of cognitive function in both groups. ALFF analysis showed that the brain activity in regions regulating motor function, vision, attention, and working memory were restored in both groups, reflecting the neuroplasticity of the brain. However, some persistent impairments and new-onset impairments in other regions related to these cognitive functions were observed in each group. Between-group comparison showed that although cognitive performance improved in both groups, the specific neural basis of LT in each group was different. The significant correlations of altered brain activity in regions showing LT and group effect with altered performance in neuropsychological and biochemical tests suggest a possible neuroimaging marker for the monitoring of short-term recovery of HE and the difference in individual recovery of cognitive performance. The findings in the present study help us further understand the neural effect of LT in patients with and without overt HE.