This research investigated the effects of tolerating nanoparticles (tNPs) loaded with multiple regulatory molecules on progression of experimental autoimmune encephalomyelitis (EAE). The polylactic acid-glycolic acid copolymer (PLGA), multiple regulatory molecular fragments (Fc) (programmed death receptor ligand 1-Fc (PD-L1-Fc), CD47-Fc), transforming growth factor (TGF-β1), and multiple oligodendrocyte glycoprotein (MOG) antigen peptides (p-MOG) were selected to prepare the tNPs (MRM-tNPs) loaded with various regulatory molecules. Then, the MRM-tNPs were applied in MOG35-55 polypeptide-induced EAE mouse model. According to the treatment methods, the mice were rolled into a group A (BS therapeutic agent), a group B (no-load-NPs), a group C (MOG-tNPs), and a group D (MRM-tNPs). The therapeutic effects were evaluated by the inflammatory infiltration degree (IID), demyelination loss degree (DLD), and apoptosis rate (AR) of CD4+ and CD8+ T cells. The Results showed that the encapsulation rate (ER) of TGF-β1 was 87.65%, and its cumulative release rate (RR) was 58.22%. There were obvious fluorescence signals on MRM-tNPs, MRM-tNPs without PD-L1, and MRM-tNPs without CD47. The neurological function (NF) score in the group D after MRM-tNPs treatment was less than 2 points (P <0.05). The scores of IID and DLD in the brain and spinal cord (SC) of EAE mice in the group D were much lower to those in groups A, B, and C, and the ARs of CD4+ and CD8+ T cells were higher (P <0.05). In conclusion, the tNPs loaded with various regulatory molecules can promote the apoptosis of antigen-specific T cells (AST) and reduce the infiltration and demyelination of inflammatory cells, thus alleviating the EAE.