BACKGROUND AND PURPOSE: Many studies have shown that insomnia is an independent factor in cognitive impairment, but the involved neurobiological mechanisms remain unclear. We used regional homogeneity to explore the specific neurobiologic indicators of chronic insomnia disorder with mild cognitive impairment. MATERIALS AND METHODS: Thirty-nine patients with insomnia were divided into a group with and without cognitive impairment; we also included a control group (n = 28). Abnormalities in brain functional activity were identified by comparing the regional homogeneity values for each brain region among the groups. RESULTS: Subjective insomnia scores were negatively correlated with cognitive impairment after controlling for age, sex, and educational effects. Regions with significant differences in regional homogeneity values in the 3 groups were concentrated in the right medial prefrontal cortex, the right superior frontal gyrus, and the left superior occipital gyrus. Meanwhile, subjective insomnia scores were negatively correlated with the strength of the decreased regional homogeneity in the right medial prefrontal cortex. The increased regional homogeneity value in the right superior frontal gyrus was positively correlated with the Montreal Cognitive Assessment score in patients. CONCLUSIONS: Our results indicate that decreased regional homogeneity values in the medial prefrontal cortex and increased regional homogeneity values in the cuneus may be important neurobiologic indicators of chronic insomnia disorder and accompanying cognitive impairment. Overall, our study described the regional homogeneity of the whole brain in chronic insomnia disorder with mild cognitive impairment and could be the basis for future studies.