Depression is a common occurrence in patients with Parkinson's disease (PD). Thus, there may be a common neural mechanism underlying the two diseases. Lewy body accumulation in specific brain areas of PD patients may damage emotion-related functions, leading to depression. Among these areas, the amygdala may present with the earliest to be damaged in PD. However, it is still unclear whether amygdala structural and functional changes are related to depression in PD. We enrolled 19 depressed PD patients, 19 non-depressed PD patients, and 28 normal control subjects. Clinical assessment, including the Unified Parkinson's Disease Rating Scale, the Hamilton Rating Scale for Depression, and the Mini-Mental State Examination, was carried out on all the patients. Structural and resting-state functional brain images were also acquired to assess volumetric and functional changes of the amygdala in the patients. Results showed that although there is no significant volume change, left amygdala activity increased in the PD group compared with the normal control group, and it correlated with Hamilton Rating Scale for Depression scores. Furthermore, functional connectivity between the right amygdala and fronto-parietal areas was found to be decreased in the depressed PD patients compared with non-depressed PD patients. These results suggest that abnormal amygdala function may underlie the occurrence of depression in PD.