Objectives: Although it is widely observed that chronic insomnia disorder (CID) is associated with cognitive impairment, the neurobiological mechanisms underlying this remain unclear. Prior neuroimaging studies have confirmed that a close correlation exists between functional connectivity and cognitive impairment. Based on this observation, in this study we used resting-state functional magnetic resonance imaging (rs-fMRI) to study the relationship between whole brain functional connectivity and cognitive function in CID. Methods: We included 39 patients with CID and 28 age-, gender-, and education-matched healthy controls (HC). Abnormalities in functional connectivity were identified by comparing the correlation coefficients for each pair of 116 brain regions between CID and HC. Results: Cognitive impairment was associated with reduced subjective insomnia scores after controlling for age, gender, and educational effects. Compared with HC, patients with CID had larger negative correlations within the task-negative network [medial prefrontal cortex (mPFC), precuneus, inferior temporal gyrus, cerebellum, and superior parietal gyrus], and between two intrinsic anti-correlation networks (mPFC and middle temporal gyrus; supplementary motor area and cerebellum). Patients with CID also had decreased positive correlations within the default mode network (DMN), and between the cerebellum and DMN, which mainly comprises the mPFC and posterior cingulated cortex. There were positive correlations of decreased positive connectivity with subjective sleep scores and MMSE scores, and increased negative correlations between the task-negative-network and MMSE scores in CID. Conclusions: Using rs-fMRI, our results support previous observations of cortical disconnection in CID in the prefrontal and DMN networks. Moreover, abnormal correlations within the task-negative network, and between two intrinsically anti-correlation networks, might be important neurobiological indicators of CID and associated cognitive impairment.