The purpose of this study was to investigate spontaneous neuron activity in spinal trigeminal nucleus (sTN) and its intrinsic functional connectivity (FC) with other key structures in migraineurs during resting-state fMRI scans. Thirty-five female migraine without aura (MWoA) during headache interictal phase and 35 age matched female HC were recruited. We found higher ALFF z-value of left sTN in female MWoA. We also found significantly weaker FC between the sTN and caudate putamen (CPu), and dorsolateral prefrontal cortex (DLPFC). Our results help us better understand the pathology of migraine.