〔Abstract〕 Objective To investigate the effect and mechanism of pituitary adenylate cyclase activated peptide recombinant 13 peptide(PACAP13) on thymus at cell, organ and individual levels. Methods Thymic epithelial cells(TEC) and bone marrow mesenchymal stem cells(MSC) were culturedin vitro, lymphocyte group, lymphocyte+TEC group, lymphocyte+MSC group and lymphocyte+TEC+MSC group were set up to detect the proliferation of lymphocytes in each group treated by PACAP13 peptide, and contents of cytokines interleukin(IL)-1, IL-2, IL-6 and transforming growth factor(TGF) in culture medium were detected. Dexamethasone(Dex) was added to induce cell apoptosis, and Annexin V-FITC/PI flow cytometry double staining was used to detect the effect of PACAP13 peptide on cell apoptosis. Thymus group, thymus+ TEC group, thymus+ MSC group, thymus+ TEC+ MSC group were set up, and PACAP13 peptide was added, the content of signal joint T cell receptor rearrangement excision cricles(sjTREC) in thymus was detected by real-time quantitative PCR(qRCR). The pristane-induced lupus model mice were randomly divided into model group and PACAP13 group. Model group was injected with 0.9% saline, and PACAP13 group was injected with PACAP13 peptide, thymus and spleen sjTREC levels were detected by qPCR, serum lupus-related autoantibodies were detected by ELISA and thymus-related mRNA expression levels were detected by reverse transcription quantitative PCR(qRT-RCR). Results Compared with the lymphocyte group, the proliferation rate of thymus lymphocytes in the lymphocyte+TEC group, lymphocyte+ MSC group, lymphocyte+ TEC+ MSC group increased, and the apoptosis rate decreased(P<0.05), compared with the control group, the proliferation rate of lymphocytes in the PACAP13 group increased, the rate of apoptosis decreased, and the cytokines IL-1, IL-2, IL-6 and TGF in the cell culture medium increased(P<0.05). Compared with the thymus group, thymus+ TEC group, thymus+ MSC group, thymus+ TEC+ MSC group increased the content of thymus sjTREC, compared with the control group, PACAP13 peptide group thymus sjTREC content increased. Compared with the model group, the content of sjTREC in the thymus and spleen of lupus mice in the PACAP13 group increased(P<0.05), thymus mRNA expression level of AIRE, Fezf2, Foxp3 and TGF-β increased(P<0.01), and CXCL13 mRNA expression level decreased(P<0.01), the autoantibodies of anti-dsDNA antibody, anti-RNP/sm antibody and ANA decreased in serum(P<0.05). Conclusion PACAP13 peptide can promote the proliferation and anti-apoptosis of thymus lymphocytes, enhance the production and output of thymus lymphocytesin vitroandin vivo, and immunomodulatory effects of reducing the level of autoantibodies in lupus mice, and the mechanism is related to the regulation of thymic cytokine secretion and gene transcription level.