Background Episodic migraine (EM) is associated with alterations in functional connectivity of several regions or resting-state networks, but it is not well known how large-scale functional connectivity pattern of the whole brain is affected in chronic migraine (CM). Methods Fifty-six migraineurs without aura (39 with EM, 17 with CM) and 35 healthy controls (HC) underwent clinical assessment and resting-state functional MRI. Functional connectivity density (FCD) was calculated in a voxel-wise way to examine large-scale brain network property over the whole brain. Results Compared with HC, both migraine groups showed increased local FCD in the left orbital frontal gyrus (OFG), right hippocampus/parahippocampal gyrus (HP/PHG), cerebellum, and decreased local FCD in the bilateral dorsolateral prefrontal cortex. Local FCD of the left OFG increased in CM compared to EM. In comparison with HC, EM showed increased local FCD in the left middle temporal gyrus, and CM exhibited decreased local FCD in the left sensorimotor cortex and bilateral precuneus. Furthermore, relative to HC, EM showed increased distant FCD in the right PHG while CM showed increased distant FCD in the right HP and OFG. Importantly, majority of the observed local and distant FCD alterations were associated with migraine frequency across all migraineurs. Conclusion Patients with higher migraine frequency present more extensive and pronounced functional connectivity dysfunctions in regions involved in pain processing and modulation. FCD, especially local FCD may be a sensitive biomarker for examining the neural mechanism of migraine.