Although previous studies reported altered topology of brain functional networks in patients with Parkinson's disease (PD), the modular organization of brain functional networks in PD patients remains largely unknown. Using the resting-state functional MRI (R-fMRI) and graph theory, we examined the modular organization of brain functional networks in 32 unmedicated patients with early-to-mid motor stage PD and 31 healthy controls. Compared to the controls, the PD patients tended to show decreased integrity and segregation, both within and between modules. This was inferred by significantly increased intra-modular characteristic path length (L (p)) within four modules: mPFC, SN, SMN, and FPN, decreased inter-modular functional connectivity (FC) between mPFC and SN, SMN, and VN, and decreased intra-modular clustering in the PD patients. Intra-modular characteristic path length within the mPFC showed significantly positive correlation with general cognitive ability in the PD group. Receiver operating characteristic (ROC) analysis revealed that FC between mPFC and SN had the highest significant accuracy in differentiating the patients from the controls. Our findings may provide new insight in understanding the pathological changes that underlie impairment in cognition and movement in Parkinson's disease.