The pathogenesis of insomnia is related to the dysfunction of the thalamus. Transcutaneous auricular vagus nerve stimulation (taVNS) has proved to be effective in treating insomnia. However, whether taVNS alleviates insomnia through modulating thalamus-related functional connectivity remains unclear. To elucidate the instant modulating effects of taVNS on the resting state functional connectivity (RSFC) of the thalamus, 20 patients with insomnia disorder were recruited to receive taVNS treatment and their resting state functional magnetic resonance imaging (fMRI) data were collected immediately before and after stimulation. The fMRI data were compared with 20 age- and gender-matched healthy subjects who received no stimulation and had RSFC fMRI data collected once. RSFC analyses of the thalamus were performed in both groups. In addition to assessing the group differences between ID patients and healthy controls regarding the RSFC of the thalamus, we examined the taVNS-induced changes of RSFC of the thalamus in ID patients. Before taVNS treatment, the ID patients showed increased RSFC of the thalamus with the right insula and inferior frontal gyrus than healthy controls. After taVNS treatment, the RSFC between the thalamus and the right angular gyrus, left anterior cingulate gyrus, and precuneus were significantly decreased in patients. This study provides insights into the instant brain effects involving the thalamus-related functional connectivity of taVNS performed on insomnia disorder patients.