Depression is the most common psychiatric disorder observed in Parkinson's disease (PD) patients, however the neural contribution to the high rate of depression in the PD group is still unclear. In this study, we used resting-state functional magnetic resonance imaging (fMRI) to investigate the underlying neural mechanisms of depression in PD patients. Twenty-one healthy individuals and thirty-three patients with idiopathic PD, seventeen of whom were diagnosed with major depressive disorder, were recruited. An analysis of amplitude of low-frequency fluctuations (ALFF) was performed on the whole brain of all subjects. Our results showed that depressed PD patients had significantly decreased ALFF in the dorsolateral prefrontal cortex (DLPFC), the ventromedial prefrontal cortex (vMPFC) and the rostral anterior cingulated cortex (rACC) compared with non-depressed PD patients. A significant positive correlation was found between Hamilton Depression Rating Scale (HDRS) and ALFF in the DLPFC. The findings of changed ALFF in these brain regions implied depression in PD patients may be associated with abnormal activities of prefrontal-limbic network.