The basal ganglia have been implicated in a modulation role in idiopathic generalized epilepsy (IGE) by an invasive electrophysiolgic means. This paper investigates the basal ganglia functional connectivity by using the region-wise functional connection analysis in resting-state functional magnetic resonance imaging (fMRI) in IGE. The increased functional connectivity within basal ganglia, and between the basal ganglia and the thalamus, and decreased functional connectivity between basal ganglia and motor cortex are found in IGE compared with the controls. These findings not only implicate dysfunctional integration in the motor loop in IGE and the enhanced interaction in the modulated loop, but also suggest that the basal ganglia modulate the generalized epileptic discharges with the influence over thalamus in the corticothalamus network.