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The mammalian nervous system controls complex functions through highly specialized and interacting structures. Single-cell sequencing can provide information on cell-type-specific chromatin structure and regulatory elements, revealing chromatin differences between different cell types and their potential roles in brain function. Here, we employed single-cells ATAC-seq to generate a chromatin accessibility dataset from 16 adult rat brain regions, obtained 174,593 high-quality nuclei. We identified cell subtypes of two cell types (neuronal and non-neuronal) with highly specific distributions and characterized gene regulatory elements associated with cell type-specific regions. To further investigate the gene regulatory network of spinal cord regeneration process, we integrated our scATAC-seq data with published single- nucleus RNA-seq data of spinal cord, identified more detailed regeneration related elements to drawGRNs centered on the transcription factor Jun in OPC. Simultaneously, we also performed similar integration analysis in midbrain. Our findings provide a solid foundation for comprehensively dissecting the molecular architecture of the mammalian nervous system.