Background: Mild cognitive impairment (MCI) is a common non-motor symptom of early Parkinson's disease (PD), but the neural mechanisms underlying it remain poorly understood. The aim of the present study was to investigate the characteristics of cognition-related brain activities in the PD patients with MCI. Methods: The brain fMRIs and cognition tests were acquired in 39 PD patients and 22 healthy controls (HC) from September 2013 to January 2015. The patients were divided into two groups: PD-MCI (n = 18) and PD with normal cognition (PDNC, n = 19). we used resting state fMRI and a regional homogeneity (ReHo) method to explore patterns of intrinsic brain activity in patients with PD-MCI as compared with PDNC subjects and HC. Results: Compared with the PDNC group, the PD-MCI group exhibited significantly increased ReHo in parts of the prefrontal cortex regions (e.g. right superior frontal gyrus, right middle frontal gyrus and orbitofrontal cortex). Compared to the HC group, a decrease of ReHo value in left thalamus was found in PD-MCI. However, this reduction was not found in the left thalamus of PDNC group, but in the above prefrontal regions (p < 0.05, with Bonferroni correction).Conclusions: These results demonstrate that the ReHo of prefrontal cortex in resting state is changed in PD patients with MCI. The presence of MCI in PD may be attributed to abnormal regional activity in prefrontal cortex regions.