Background Huntington's Disease (HD) is characterized by motor, cognitive and psychiatric dysfunction. Functional MRI (fMRI) provides new insight into the pathologic mechanism underlying the cognitive symptoms. Previous fMRI studies of HD focused on functional synchronization of various brain areas by measuring functional connectivity, a method that is unable to identify regional intrinsic neural activity changes in the brain. To fill in this gap, we utilized amplitude of low frequency fluctuations (ALFF). Objective To investigate alterations in regional brain activity and their association with clinical characteristics in the early stages of HD. Methods Ten early stage HD patients and 20 age- and sex-matched healthy controls were scanned to obtain imaging data. HD patients were assessed with the Unified Huntington's Disease Rating Scale, Mini-Mental State Exam (MMSE), Stroop test, Symbol Digit Modalities Test (SDMT), Verbal Fluency Test and Beck Depression Index. Results Gray matter volume (GMV) reduction was detected in bilateral striatum and left calcarine cortex in the HD group. After correcting for GMV, HD patients demonstrated significantly decreased ALFF in the right precuneus and angular gyrus, and increased ALFF in bilateral inferior temporal gyrus (ITG) and left superior frontal gyrus. Increased mean values of ALFF in the left ITG were correlated with worse performance in SDMT, and decreased mean values of ALFF in the precuneus were correlated with worse performance in the Stroop test and SDMT. Conclusions Our results suggest that intrinsic brain activity alterations in the precuneus and cortico-striatal circuit may be the mechanism underlying impaired cognition in early HD.