Insomnia is a common mental illness seriously affecting people lives, that might progress to major depression. However, the neural mechanism of patients with CID comorbid MDD remain unclear. Combining fractional amplitude of low-frequency fluctuation (fALFF) and seed-based functional connectivity (FC), this study investigated abnormality in local and long-range neural activity of patients with CID comorbid MDD. Here, we acquired resting-state blood oxygenation level dependent (BOLD) data from 57 patients with CID comorbid MDD and 57 healthy controls (HC). Compared with the controls, patients with CID comorbid MDD exhibited abnormal functional activity in posterior cerebral cortex related to the visual cortex, including the middle occipital gyrus (MOG), the cuneus and the lingual gyrus, specifically, lower fALFF values in the right MOG, left cuneus, and right postcentral gyrus, increased FC between the right MOG and the left cerebellum, and decreased FC between the right MOG and the right lingual gyrus. Neuropsychological correlation analysis revealed that the decreased fALFF in the right MOG was negatively correlated with all the neuropsychological scores of insomnia and depression, reflecting common relationships with symptoms of CID and MDD. While the decreased fALFF of the left cuneus was distinctly correlated with the scores of depression related scales. The decreased FC between the right MOG and the right lingual gyrus was distinctly correlated with the scores of insomnia related scales. This study not only widened neuroimaging evidence that associated with insomnia and depressive symptoms of patients with CID comorbid MDD, but also provided new potential targets for clinical treatment.