Background: Primary insomnia is a high prevalent sleep disorder. Disturbed brain activity during reward, emotional, and cognitive processing have been observed in insomnia patients. Studies have implicated a critical role of the striatum in these dysfunctions. However, there have been no direct investigations on the whole-brain functional connectivity (FC) of the striatum in insomnia. Methods: We analyzed the group differences in the FC images of 6 predefined striatal subregions based on the multi-band resting-state fMRI data of 18 insomnia patients and 16 healthy controls. Results: We found increased positive FC in the bilateral medial frontal gyrus for bilateral dorsal caudate (DC) and left inferior ventral striatum (VS) subregions, but increased negative FC in the bilateral inferior parietal lobe for the left inferior VSi and right dorsal caudal putamen (DCP) subregions, and in the lateral temporal, occipital, and primary sensorimotor areas for the bilateral DC and left superior VS subregions. The FC between the right DCP and right inferior parietal lobe showed significant positive correlation with Pittsburgh Sleep Quality Index (PSQI). Conclusion: The findings indicate disturbed striatal FC with the default mode network (DMN), the visual and somatosensory areas in insomnia, which likely reflects an inappropriate reward or emotional significance attribute to self-reflection, episodic memory, sensory-perception processes. The altered striatal FC might increase the risk of insomnia patients to develop depression and anxiety.