Cyclosporine A (CsA) is a widely known immunosuppressive agent that is clinically important in autoimmune diseases owing to its selective suppression of T lymphocytes. Although it has long been recognized to inhibit T cell responses by blocking calcineurin, the potential targets and specific downstream mechanisms remain elusive. Herein, we built a comprehensive single-cell transcriptomic landscape of immune cells in the blank, untreated experimental autoimmune uveitis (EAU), and CsA-treated EAU mice. CsA reversed EAU-associated changes in cell type composition, genomic expression, cell trajectory, and cell-cell communication. We found that CsA reverses the proportion change of disease-related immune cells; regulates several crucial pathogenic factors (eg. IL1r1, CD48, and Bhlhe40) in T helper 17 cells (Th17), the transcription factor Bhlhe40 was also rescued in T helper 1 cells (Th1); and may differentiate Tregs into a state of enhanced immunosuppression. In addition, we revealed the rescued impact of CsA on all immune cell types, especially on plasma B cells differentiation and immunoglobulin secretion. Furthermore, comparisons with glucocorticoids showed that CsA might have a more premium rescue effect involved in attenuating the pathogenicity of autoreactive T cells. Our work provides a comprehensive single-cell transcriptional atlas of immune cells under CsA therapy, providing advanced insights into the mechanisms underlying CsA and a reference for developing new therapeutic strategies for autoimmune diseases.