Cognitive deficits in Parkinson’s Disease (PD) are associated with abnormalities in functional brain networks that can be observed at rest. This study investigates whole-brain independent functional-connectomes in PD patients with mild cognitive impairment (PD-MCI), associating these functional connectomes with cognitive and anthropometric measures using partial least squares (PLS) regression. We found a clear distinction between two sets (PLS-components) with functional connectomes either linked to cognitive scores or anthropometric variables. A PD-specific subcortical-cortical functional connectome was common in the two PLS-components. Furthermore, in PD-MCI a functional connectome defined by attentional and sensorimotor regions linked to attention and memory deficits is critical.