Microglia are key mediators in CNS demyelinating neurodegenerative diseases, controlling the disease environment by inhibiting or favoring CNS repair. Here we combine single-cell RNA-sequencing of cortical microglia and brain bulk RNA-sequencing, together with 3D brain imaging in experimental cuprizone demyelination to provide a longitudinal characterization of brain transcriptome and microglia signatures during disease progression and remyelination. First, brain RNA-sequencing of healthy, demyelination and remyelination states revealed upregulation of microglia genes involved in inflammation, phagocytosis and lysosomal activity and sharp downregulation of myelin and neuronal genes, followed by recovery-related genes. Additionally, correlation analysis of demyelination transcriptome with diverse CNS neurodegenerative disorders revealed a common core genetic profile. Second, single-cell RNA-sequencing provided a detailed characterization of cortical microglia signature in early demyelination. Both transcriptomic approaches revealed a strong induction of disease-associated microglia (DAM), primarily described in Alzheimer’s disease, throughout demyelination and remyelination, while single cell resolution analysis allowed us to identify a disease-specific DAM microglia cluster in early cortical demyelination. Interestingly, inflammatory microglia markers were globally expressed, revealing potential molecular targets for modulating microglia responses in CNS demyelination. To target a major pro-inflammatory pathway, we applied time- and cell-specific tamoxifen-induced gene editing of TNF receptor 1 (TNFR1) in microglia in vivo. Therapeutic deletion of microglia TNFR1 was sufficient to accelerate the resolution of DAM signature and promote cortical remyelination and motor recovery. Overall, this study maps the longitudinal transcriptome signature of microglia during experimental demyelination and remyelination, and highlights the therapeutic potential of targeting inflammatory microglia to enhance CNS repair.