Background: Parkinson's disease (PD) is often associated with cognitive impairment. However, the neural mechanism of cognitive impairment is not clear. The present study investigated the functional and anatomic changes in PD patients with mild cognitive impairment (MCI) and their correlations with cognitive functions by the application of combined functional and structural analysis. Methods: T1-weighted magnetic resonance imaging (MRI) and resting-state functional MRI data were acquired from 23 PD patients with MCI (PD-MCI), 23 PD patients with normal cognitive function (PD-NCI), and 23 matched healthy controls (HC). The structural imaging data was analyzed by voxel-based morphometry (VBM) and surfaced-based morphometry (SBM) methods to assess the changes of gray matter density and cortical thickness, respectively. And the amplitude of low-frequency fluctuations (ALFF) analysis using resting-state functional imaging data to measure the spontaneous changes of brain activity. Their Correlations with neuropsychological assessments (e.g., Montreal cognitive assessment, MOCA; Mini-mental state examination, MMSE) were also examined. Results: Compared to the HC group, the PD-MCI patient group showed both decreased ALFF in the occipital regions (i.e., left middle occipital gyrus) and parietal regions (i.e., left precuneus) and increased ALFF in the right inferior frontal gyrus and bilateral hippocampus. Also, the PD-MCI patient group showed reduced gray matter density in the right inferior frontal gyrus and middle frontal gyrus. Cortical thinning in the left middle temporal gyrus and right superior temporal gyrus was found in the PD_MCI patient group relative to the control group. Furthermore, ALFF of the right hippocampus and gray matter density of right frontal gyrus was correlated with cognitive impairment (e.g., MOCA ), respectively. Cortical thickness of right superior temporal gyrus was also associated with cognitive deficit (e.g., MMSE ). Conclusion: MCI in PD is associated with widespread brain functional and structural alternations. The combination of functional and structural abnormalities may be related to subtle cognitive impairment in PD.